The hydrological processes play an important role in stimulating fish spawning behavior. Changes in the natural hydrological processes will alter the populations and distribution of fish, which may have a negative impact on the native aquatic organisms. The aim of this study is to identify the alteration of the water rising process during the fish spawning period and to construct an ecological flow optimization model to restore the water rising conditions for fish reproduction. The Mann–Kendall test and the sliding t-test were used to detect the mutation year of the mean daily flow data sets in the fish spawning period in each monitoring year. Then the data sets can be divided into pre-altered and post-altered periods. The water rising process was characterized by the water rising processes count, the duration, the daily flow increase rate, the date of the water rising process, and the initial water rising flow. The changes in hydrological processes in the middle reaches of the Yangtze River were investigated by comparing the post-altered and pre-altered characteristic parameters. Furthermore, we integrated the statistical values of the five characteristic parameters in pre-altered into an ecological flow optimization model to simulate the natural water rising processes for the spawning of the Four Major Chinese Carps (FMCC) and Chinese Sturgeon (CS). The analysis showed that after the hydrological mutation year, the duration and the initial water rising flow in the FMCC spawning season were increased, with hydrological alteration degrees of 63.10% and 70.16%, respectively; however, the daily flow increase rate was significantly decreased, with hydrological alteration of 86.50%. During the CS spawning season, the water rising processes count and the initial water rising flow were dramatically altered parameters, with hydrological alteration degrees of 50.86% and 83.27%, respectively. The former parameter increased, but the latter decreased significantly in the post-altered period. To induce the spawning activity of FMCC and CS, appropriate ecological flows and hydrological parameters were proposed. These results showed that during the spawning seasons of FMCC and CS, the hydrological processes of the middle reaches of the Yangtze River changed significantly. Therefore, ecological flow must be ensured through ecological operation of upstream reservoirs to provide suitable spawning conditions in target fish spawning grounds.