Hydraulic conductivity is the key variable in subsurface configuration that is important in modeling groundwater and its interactions with land surface processes. However, an acquisition of quantitatively distributed hydraulic conductivity is challenging due to limitations on data availability, accuracy and resolution, which inhibits an advanced understanding of hydrologic and energy cycles at the basin scale. This study investigated the role of hydraulic conductivity in simulating groundwater-land surface interactions over a typical endorheic river basin in northwestern China. A 3D variably saturated groundwater model coupled to a land surface model was configured to account for interactions between groundwater dynamics and land energy fluxes. Four scenarios of hydraulic conductivity were tested and inter-compared, adopting both homogeneous and heterogeneous parameterization strategies based on Global Soil Dataset for use in Earth System Models (GSDE) and HYdrogeology MaPS (GLHYMPS). The overall objectives are to diagnose effects of hydraulic conductivity on simulating groundwater–land surface interactions, with a particular focus on differences in spatial distributions and statistical characteristics between scenarios, as well as the dynamics and feedback mechanisms between groundwater and land surface energy fluxes. Comprehensive simulations and analyses were conducted to discern spatial distributions and statistical characteristics of key hydrological variables (streamflow, water table depth, latent heat flux, sensible heat flux) under different scenarios. Results showed that the hydraulic conductivity of the saturated zone had a significant control over water table depth, while the combine hydraulic conductivity in the vadose zone and the saturated zone governed the evolution of streamflow. Moreover, the water table critical range—where the land energy budget is highly sensitive to groundwater table—was 0.1 m–5 m and the area might expand approximately 4.5 % after considering the heterogeneity of hydraulic conductivity. Compared to the homogeneous scenario, the spatial heterogeneity of hydraulic conductivity amplified water table depth variability while diminishing land energy fluxes variability.