In order to improve the cognition of hydrogeology and groundwater resources in the Yangtze River Basin and break through the limitations of previous evaluation from the point of view of surface water or groundwater, the hydrogeology survey project in the Yangtze River Basin was guided by the earth system science theory and water cycle theory. Based on the full consideration of the transformation relationship between surface water and groundwater, hydrogeology unit and surface water basin were organically combined to divide groundwater evaluation units in the Yangtze River Basin. A new round of groundwater resource evaluation in the Yangtze River basin was carried out through the establishment of typical groundwater resource evaluation model. The evaluation results show that the spatial and temporal distribution of water cycle elements in the Yangtze River basin is uneven, with the highest precipitation in the middle reaches and decreasing from southeast to northwest. Surface runoff is mainly concentrated in summer, the north bank is higher than the south bank in summer concentration surface runoff. Evapotranspiration is generally higher in the east than in the west, and the maximum value is concentrated in the middle reaches of the Yangtze River. The groundwater level in the Yangtze River basin remains stable on the whole, and the water level changes little in the peak and dry seasons, generally less than 2 m. The area of groundwater funnel in the Yangtze River Delta over-exploitation area has been significantly reduced, and the related environmental geological problems have been effectively controlled. In 2020, the total groundwater resources in the Yangtze River Basin was 242.170 billion m³/a, including 209.279 billion m³/a in hilly areas and 33.135 billion m³/a in plain areas. Compared with 2019, the groundwater storage increased slightly, especially in Sichuan Basin, with a total increase of 2.372 billion m³. The water quality in the upper reaches of the Yangtze River basin is better than that in the lower reaches, and the high-quality groundwater is mainly distributed in southern Jiangxi and the western foothills of Dabie Mountains. The main reason for poor water quality in some areas is the widespread distribution of primary inferior water. The development and utilization level of groundwater in the Yangtze River Basin is very low as a whole. The environmental geological problems caused by unreasonable development in some areas have been greatly solved, and karst collapse and land subsidence have been well controlled. It is suggested that high-quality bedrock fissure water should be properly developed and utilized in southern Jiangxi and south Dabie Mountains.