Abstract: The mutual transformation of surface water and groundwater is an obvious feature of water cycle in arid inland basins in northwest China. Examination of the transformation mechanism is an important basis for the cognition of basin water cycle law and the sustainable management of water resources. In this paper, the Zhangye Basin and Yanchi Basin in the middle reaches of the Heihe River Basin in the arid inland river of northwest China are taken as the research areas, and the time-varying water balance model of the main channel of the Heihe River and the coupling numerical model of surface water and groundwater are established. The conversion mechanism of surface water and groundwater under the dual influence of long-term hydrological changes and human activities is studied, and the following understanding is obtained. (1) The recharge conditions change from linear recharge dominated by river leakage under natural conditions to linear recharge dominated by river and diversion channel leakage and surface recharge of infiltration in irrigation areas. The discharge conditions change from spring overflow and natural wetland discharge to spring overflow and groundwater exploitation. (2) The infiltration section and overflow section of the Heihe River in the Zhangye Basin are roughly bounded by the G312 Bridge, which is also called the turning point of surface water and groundwater transformation. The Yingluoxia-G312 bridge section is a suspended river leakage section, and the river infiltration recharge is mainly controlled by the actual amount of water entering the river. Among them, the infiltration recharge rate of the Yingluoxia-Caotanzhuang section is 43.34%. The river channel infiltration recharge and river channel flow can be expressed by the piecewise function in the Caotanzhuang-G312 bridge section. When the river channel flow is greater than (or equal to) and less than 3.7×10⁸ m³ per month, it shows a power function relationship and a linear function relationship, respevtively. The G312 bridge-Zhengyixia section is the groundwater overflow section. The groundwater overflow amount of the G312 bridge-Pingchuan bridge section accounts for about 70% of the total overflow amount. The peak overflow occurs at about 6 km downstream the Gaoya hydrological station, and the single-length overflow amount can reach 0.46 m³/(s·km). (3) The study area is a relatively complete river-aquifer system, which has undergone continuous dry and wet hydrological changes in the past 31 years. The recharge and discharge conditions of groundwater and the transformation mechanism of surface water and groundwater have changed accordingly. The conversion between surface water and groundwater is the strongest in the Heihe-Liyuan River inclined plain in the middle of the Zhangye Basin. During the continuous dry period from 1990 to 2001, the water diversion in the irrigation area decreased year by year, and the recharge mainly caused by river channel infiltration and canal system leakage decreased at a rate of 0.06×10⁸ m³/a. The increase of farmland irrigation area led to the increase of irrigation water, the obvious increase of groundwater exploitation, the decrease of groundwater level year by year, the cumulative decrease of storage amount by 5.80×10⁸ m³, and the annual decrease of groundwater overflow amount by 0.13×10⁸ m³/a. During the continuous harvest period from 2002 to 2020, the water diversion in the irrigation area decreased year by year, and the river infiltration showed an increasing trend. The total groundwater supply increased by 0.15×10⁸ m³/a, the irrigation area continued to expand, and the agricultural irrigation exploitation increased accordingly. The increase in river infiltration was the dominant factor, and the groundwater levels continued to rise. The total storage increased by 5.42×10⁸ m³, and the groundwater overflow increased by 0.06×10⁸ m³/a. In short, the recharge and discharge conditions vary greatly, the groundwater storage decreases first and then increases, and the total amount of groundwater overflow changes gently, which reflects the huge storage function of the thick aquifer system in this area. (4) The groundwater level in the production period of the inclined plain located in the eastern part of the Zhangye Basin is in a continuous decline, which is due to the sharp decrease of excessive surface water development. The groundwater level in the Heihe erosion-accumulation plain is basically stable. Over the past 30 years, the groundwater level in the inclined plain of the Yanchi Basin has been in a state of continuous decline, which is caused by excessive groundwater exploitation due to immigration reclamation. (5) The natural suspended river infiltration section in the inland basin is a precious groundwater recharge channel. Whether in the continuous dry or wet period, the actual river flow is the key to the river leakage recharge. Protection of the upstream natural river and a certain actual river flow is the key to the sustainable management of water resources in the inland basin.