The Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) is a critically endangered species, as the whole population in the wild suffered sharp decline and fragmentation. Observations of the local spatial and temporal distribution dynamics can help establish better conservation strategies. In order to understand the characteristics of habitat chosen, a continuous 15 months observation on the distribution patterns of the Yangtze finless porpoise at the confluence of Yangtze and Wanhe rivers was conducted. The results showed that the distribution of the porpoise changed seasonally. From October 2013 to March 2014 and from December 2014 to January 2015, the observation rate ranged from 12.5% to 100% of each observation day, with the average being 60%. The average maximum number of individuals observed per day was 4 (range, 1–8). Porpoises was not observed in September 2013 and from April 2014 to September 2014. Spatial distribution dynamics analyses showed that from the six different hydrological zones of the confluence, the porpoise was more likely to prefer the flow deflection and flow stagnation zones of the confluence. The average occurrence rate in the flow deflection and flow stagnation zones was 32% and 44%, respectively. Based on these observations, we concluded that the confluence of the Yangtze and Wanhe rivers is a popular habitat of the Yangtze finless porpoise in autumn and winter. Conservation measures should be taken to conserve this kind of habitat.