Abstract: Characterizing fractured aquifers plays a crucial role in the issues related to groundwater contamination, and geothermal and hydrocarbon resource exploitation. Due to the heterogeneity of the fractured medium, the permeability of fractured medium generally exhibits significant non-Gaussian characteristics, leading to difficulties and challenges in the estimation of hydrogeological parameters. This study used the ESMDA-DS (ensemble smoother with multiple data assimilation-direct sampling) integrating hydrogeophysical data to explore the effectiveness of the data assimilation framework in portraying the parameter field of the fractured medium and to analyze the influences of assimilating three different types of observation data, the fracture density, and the number of observation wells on the parameter estimation. The results show that the method of ESMDA-DS integrating hydrogeophysical data can estimate the spatial distribution of hydrogeological parameters in the fractured medium effectively. Comparing the estimated results from three types of observation, it finds that fusing the hydraulic head and the self-potential observational data (hydrogeophysical data) has the best effect. The fracture density in the study area and the number of observation wells also affect the data assimilation results. A reasonable number of observation wells is suggested to obtain the optimal parameter estimation scheme in practical applications. This study can provide an effective method for characterizing the parameter field of the fractured medium and a reliable theoretical basis for the development and management of fractured water resources.