On the basis of the current situation and history of groundwater resources evaluation in the Pearl River Basin, the water resources evaluation methods and zoning principles were discussed, and 129 four level groundwater systems are divided. Taking the groundwater system as the evaluation unit, based on the full consideration of different hydrogeological parameters, this paper analyzes and evaluates the amount of groundwater resources and the existing problems, discusses the characteristics of different flow movement in the three terraces of the Pearl River Basin, and expounds the accuracy of the evaluation and the influence of water conservancy projects on groundwater circulation. Through this evaluation, the natural groundwater resources in the Pearl River Basin are 137.416 billion m³, the exploitable amount is 57.87 billion m³, and the development and utilization rate is only 9.8%. The Pearl River Basin has a large span, and its hydrodynamic characteristics are quite different, characterized by the deep valley area in the upper reaches of Yunnan-Guizhou Plateau, the peak cluster depression area in the middle reaches of Guangxi, and the alluvial proluvial plain area in the lower reaches. According to incomplete statistics, there are 32 reservoirs in the Pearl River basin with a storage capacity of more than 1 million m³. The construction of water conservancy projects and the regulation and distribution of water resources by reservoirs bring some difficulties to the evaluation of groundwater resources. The main problems are the inconsistency of the basin boundaries between surface water and groundwater caused by the differences in the concepts of surface water and groundwater between different ministries and commissions. Therefore, the countermeasures and methods to solve the problems are put forward, so as to provide reference for the development, utilization, control and protection of groundwater.