Water flow changes lead to changes in river eco-hydrological regime, and then affect the health of river ecosystems. In order to clarify the effects of hydrologic alterations on fish habitat in the Wujiang River mainstream, daily flow data from 1956 to 2019 and spawning data of 12 drifting fish species from 2009 to 2015 were selected from the record in the Wulong Hydrological Station. The Mann-Kendall(M-K) test and the cumulative anomaly method were used to study the abrupt changes in the Wujiang River mainstream, in order to analyze the change trend of daily flow before and after the abrupt changes. Then the characteristics and change degree of 32 sets of hydrological indexes were evaluated using indicators of hydrologic alteration-range of variability approach (IHA-RVA) method, so as to study the fish population change process under the change of hydrological regimes. The results show that the abrupt change in the Wujiang River flow occurred in 2009, which is the same as the operation time of Pengshui Hydropower Station. After the abrupt change, the average daily peak flow fluctuated around 15, 000 m3/s, which was close to 18, 000 m3/s, the daily peak flow before the abrupt change. Furthermore, the overall change degree of 32 sets of hydrological indexes was 38.7%, which fell into the moderate range. The duration and frequency of low flow with high change range were 74.64% and 75.29% respectively, and the occurrence time was delayed by 4 days; whereas those of the high flow was 29.79% and 37.83% respectively, and the occurrence time was 21 days ahead. It is found that rainfall was positively correlated with discharge with great significance, so the annual decrease of rainfall had seriously affected the discharge. In addition, the variation of hydrological regimes is easily affected by Pengshui Hydropower Station. However, the impact of the hydrological regime change and reduced flow on fish is a cumulative process, the spawning scale of the 12 drifting fish species started to decrease from 2009, then dropped dramatically in 2011, which was only accounted for 15, 416, 900 eggs. These findings can provide a reference for the study of hydrological regime change process of the Wujiang River and the formulation of water ecological restoration measures.