Climate changes and human activities have led to significant variations in the hydrological conditions in Pearl River drainage basin. Distributions of flood frequencies before and after the hydrological change are significantly different. We used moving rank sum test (Mann-Whitney U test) and Brown-Forsythe, Sliding T, Ordered Cluster, and Mann-Kendall (MK), with cumulative departure curve method (CSDMC) for annual maximum discharge (AMD) details, to analysis hydrological changes and their causes. Then, L-moment was used to evaluate the parameters of generalized extreme value distributions of the whole, before and after the hydrological changes of annual maximum discharge series. The design flow values of different return periods were calculated. Results show that:(1) Hydrological changes at the stations in Beijiang River and most of Xijiang River occurred in 1991, and hydrological regulation of the three big reservoirs was the main factor in Dongjiang River. (2) After hydrological change, annual maximum discharge and flow peak intensity were increased in Xijiang River and Beijiang River, especially in the main stream of Xijiang River while opposite situation occurred in Dongjiang River. (3) After hydrological change, flood risk had been increased in Xijiang River and Beijiang River. In particular, because the Pearl River Delta region itself has been strongly affected by human activities, persistently increased flood intensity had occurred in the Xijiang River and Beijiang River. The Pearl River Delta floods and flood frequency had been increased significantly, while flood risk had been decreased in Dongjiang River. This study is very important for assessing the flood risks and flood disasters in the Pearl River drainage basin.