Abstract: Recently, some travertine landscape groups in Huanglong Scenic Spot have been degraded to varying degrees. Surface water leakage, blackening and desertification have occurred on a large scale in the dense distribution area of Salix cupularis shrub, which has adversely affected the core value of the Huanglong World Natural Heritage Site. The relationship between shrub expansion and leakage enhancement has not been fully understood. In this study, travertine pool group of typical shrub area was selected in the north of Yingyue Pool in the upper reaches of Huanglong, and 4 shrub cover levels were set: no shrub (coverage <10%), little shrub (coverage 10%−30%), many shrub (coverage 30%−60%), and whole shrub (coverage >60%). In-situ infiltration test was conducted to determine the leakage intensity and to evaluate the changes of travertine pore structure and permeability parameters in shrub area. With the comparison of the leakage intensities in different shrub cover level areas, the mechanism of surface water leakage of travertine under the influence of Salix cupularis scrub is summarized. The results show that (1) the leakage intensity increases with the increase of coverage. When the coverage of Salix cupularis shrub exceeds 60%, the leakage intensity changes significantly, which should be related to the rapid diversion of large pores. (2) Under the influence of algae activities and decomposition of plant residues, new travertine with more pores and holes is formed in the scrub area, resulting in higher natural leakage intensity than that in the non-scrub area. (3) The root activities of Salix cupularis shrub changes the primary travertine structure, leading to loose primary travertine and increases of pore diameter, effective porosity, and permeability coefficient. The enhanced groundwater seepage resulted in enhanced overall surface water leakage in the travertine pool. (4) The transformation of travertine pore structure by Salix cupularis roots is depended on the root cleavage. The dissolution of travertine cement by root solution leads travertine to uniform loose accumulation. The results show that the root and algal activities in Salix cupularis scrub area mainly control the process of surface water leakage enhancement. This study have basic value for the evolution analysis and conservation of Huanglong travertine natural heritage landscape.