The surface watershed and groundwater basin have fixed recharge scale, which are not only the basic unit for hydrologic cycle research but also control the water resources formation and evolution and its corresponding eco-geological environment pattern. To accurately identify the boundary of the surface watershed and groundwater basin is the basis for properly understanding hydrologic cycle and conducting the water balance analysis at watershed scale in complicated geologic structure area, especially when the boundary are inconsistent. In this study, the Dalinuoer Lake located in the middle of the Inner Mongolian Plateau which has complicated geologic structure was selected as the representative case. Based on the multidisciplinary comprehensive analysis of topography, tectonics, hydrogeology, groundwater dynamics and stable isotopes, the results suggest the following: (1) The surface watershed ridge and groundwater basin divide of Dalinuoer Lake are inconsistent. The surface watershed was divided into two separate groundwater systems almost having no groundwater exchange by the SW-NE Haoluku Anticlinorium Fault which has obvious water-blocking effect. The surface drainage area of Dalinuoer Lake is 6139 km2. The northern regional A is the Dalinuoer Lake groundwater system with an area of 4838 km2, and the southern regional B is the Xilamulun Riverhead groundwater system with an area of 1301 km2. (2) The groundwater in the southern of regional A and the spring-feeding river are the important recharge sources for the Dalinuoer Lake, and it has greater recharge effects than the northern Gonggeer River system. (3) It is speculated that the trend of Haoluku Anticlinorium Fault is the boundary of the westerlies and the East Asian summer Monsoon (EASM) climate systems, which further pinpoints the predecessor’s understanding of this boundary line. At present, the Dalinuoer Lake watershed is proved to have gone through a prominent warming-drying trend periods, which leads to the precipitation reduction, temperature rise, human activities water usage increasement. So the hydrological cycle and lake eco-environment at watershed scale will still bound to be change, which may pose the potential deterioration risk on the suitability of fish habitat. The results can provide basic support for better understanding water balance evolution and lake area shrinkage cause as well as the ecological protection and restoration implementation of Dalinuoer Lake watershed.