The Yangtze finless porpoise, a distinct species inhabiting the middle and lower reaches of the Yangtze River in China, has displayed indications of population stabilization and recovery in two recently ecological surveys. However, it remains critically endangered. To further reinforce the positive trajectory of porpoise population growth, preserving an optimal habitat is indispensable for the conservation of this species. Nevertheless, the intricate hydrological conditions, channel regulation, shoreline development, and projects like a decade-long fishing ban may affect the porpoise habitats in the lower Yangtze River. Therefore, conducting surveys and habitat assessments for the Yangtze finless porpoise in the lower reaches is of significant importance. This study utilized boat surveys combined with environmental DNA monitoring to offer preliminary insights into the population distribution, activity patterns, and environmental characteristics of the Yangtze finless porpoise in the lower Yangtze River, Nanjing to Zhenjiang reach. By integrating variously critical habitat factors including water depth, flow velocity, shoreline, and prey availability, a physical habitat model for the Yangtze finless porpoise in the lower reaches was established, which was used to simulate and analyze the suitability of the porpoise habitat. The results show that both ship surveys and environmental DNA monitoring reveal that the finless porpoises are mainly distributed in the Nanjing protected area, followed by the non-protected area, and the Zhenjiang protected area has fewer occurrences. The sequence abundance of finless porpoises is the highest at the Green Water Bay Park site, accounting for 7.77%, and the gene copies number is the highest at the Lieshan site, reaching 22.56 copies/?L. Observation points with high porpoise occurrence and abundance align with the model’s prediction of suitable habitats, demonstrating the model’s capability to simulate porpoise habitat suitability. The overall habitat suitability is higher in the Nanjing section, encompassing a significant area. Finally, to safeguard porpoise habitats in the Nanjing downstream deep-water channel project, it is advisable to thoroughly incorporate ecological measures in the subsequent channel regulation projects, supporting the Yangtze River Conservation and the coordinated development of the national strategy for the Yangtze Economic Belt.