Considering limited manpower, funding, and land available for conservation projects, selecting a set of key areas to maintain biodiversity is important. The Yangtze River Basin (YRB) is a globally significant center for biodiversity but faces many threats and pressures. Previous research attempted to identify conservation gaps in the YRB based solely on species distribution in terrestrial ecosystems. This study focused on wetland ecosystem conservation patterns on an entire river basin scale. Systematic conservation planning (SCP) is a framework that has been developed to prioritize and manage habitats deemed important for the protection of natural values. We used SCP methods to define watersheds as planning units and developed a comprehensive map of wetland types, considering climatic factors and geomorphological factors as coarse-filter surrogates of biodiversity elements, which included 28 wetland classes. We integrated the distribution of 113 focal birds as fine-filter surrogates of biodiversity elements. Marxan is a software used to determine the optimal set of planning units to form a pattern that meets the protection target with the minimum of social economy cost and land resources. We used Marxan to identify a conservation priority pattern by calculating the irreplaceability of each unit. Then, we compared the priority pattern with the existing reserve system to analyze conservation gap in the YRB. The results showed that the wetlands at the source of the YRB are large and well-protected; the proportion of protected wetlands in the Jinshajiang sub-basin arrived at 38.74% in the priority pattern, improved by 19.74% compared to the existing protection system. The protected proportion in the Ming-Tuo sub-basin is 7.05% at present, and improved to 22.08% after the optimization; the priority protection areas are mainly distributed in Sichuan. The additional proportions in the Jialinjiang sub-basin and the upper mainstream sub-basin are large with conservation gaps mainly distributed in Sichuan province; Dongting Lake Basin and Hanjiang sub-basin are relatively well-protected. The protected proportion of wetlands in the Poyang Lake basin can rise from 7.10% to 28.49% with the additional proportion rising up to 40.89% in the Taihu sub-basin; most conservation gaps in the middle and lower reaches of the Yangtze River were distributed among riparian wetlands. In summary, the main conservation gaps are distributed in Chongqing, Guizhou, Hunan, and Hubei provinces. The results provide a reference for conservation planning in the YRB. Moreover, the identification of priority conservation areas on a large scale can be used to influence the building of a well-connected protection network in each individual area. For conservation gaps in the middle and lower reaches of the Yangtze River, we can build wetland parks and restore the river bank. For small conservation gaps distributed around existing reserves, we can extend the boundary of the reserves or adjust their scope. The results provide decision makers with scientific evidence for conservation planning for Yangtze River wetlands, and enrich the examples of SCP for freshwater wetlands.