The Yangtze finless porpoise (Neophocaena asiaeorientalis) is a critically endangered freshwater cetacean endemic to the Yangtze River, China. Habitat loss and fragmentation caused by anthropogenic disturbance such as waterway regulation engineering can be the most influential factor threatening the Yangtze finless porpoise population. Previous studies mainly focused on effects of existing hydraulic structures on distribution of the Yangtze finless porpoise. For their habitat conservation, it is essential to understand spatio-temporal effects of waterway regulation engineering on population abundance and distribution of the Yangtze finless porpoise. In the present study, 12 population surveys were conducted from December 2015 to December 2021 on Hukou-Jiyangji section of the Yangtze River, in which an Anqing waterway regulation engineering was implemented from January 2019 to April 2021. Among them, there were 5 visual surveys conducted in pre-construction stage, 5 in construction stage, and 2 in post-construction stage. Through the whole study, 613 finless porpoises were observed in 258 sightings in the whole survey area. In a single survey, averages of observed porpoises were 67.0±24.3, 35.6±22.2 and 50.0±2.8 in pre-construction, construction, and post-construction stages, respectively. In the main construction area, 185 individuals were observed in 79 sightings, and averages of observed porpoises were 18.60±12.03 in pre-construction stage, 10.4±7.3 in construction stage, and 20.0±4.2 in post-construction stage, among which no significant difference was detected. These inferred that the waterway regulation engineering would not cause obvious porpoises abundance decline in the main construction area in short term. In the main construction area, population density in engineering sections S2 and S3 decreased significantly in construction stage (S2:0.18±0.17 ind./km, S3:0.04±0.08 ind./km) from pre-construction stage (S2:0.62±0.16 ind./km, S3:0.40±0.29 ind./km). In engineering sections S5 and S6, no significant decreases were detected between population density in construction stage (S5:0.22±0.31 ind./km, S6:0.36±0.28 ind./km) and pre-construction stage (S5:0.28±0.43 ind./km, S6:0.78±0.81 ind./km). In post-construction stage, the population density was recovered to a great extent in S2, S5 and S6, except for S3 due to the high habitat destruction. During construction and post-construction stages, porpoises distribution continuity decreased by gathering to undisturbed habitat patches. Our findings indicated porpoise population might be not impacted during the construction and operation of waterway regulation engineering, but hydraulic constructions destruct their habitat could lead to fragmentation of population distribution. The waterway regulation engineering should detour porpoises' suitable habitats and preserve natural continuity of habitat patches, to reduce the risk of migration obstruction and population fragmentation.