Abstract: Yellow River basin is a significant habitat for biodiversity conservation in China. Here, we established a integrated classification system of wetlands based on climate types and geomorphological units, with which as the coarse-filter surrogates of biodiversity elements to complement the fine-filter surrogates of distribution of focal bird species. Then, we applied the theoretical framework of systematic conservation planning (SCP), with those two biodiversity surrogates as protection objects and watershed as planning units. We calculated social and economic costs (including roads, railroads, towns, rural settlements, dams) and set targets of 30% to input Marxan to figure out the optimal set of planning units, which met the protection target with the minimum of social economy cost and land resources. We identified a conservation priority pattern by calculating the irreplaceability of each unit by Marxan. Then, we compared the priority pattern with the existing reserve system to analyze conservation gap in the Yellow River basin. The results showed that most marsh wetlands were concentrated in the upper reaches of the Yellow River. The coverage of reserves in the source area was large. Some rare wetland types in Inner Mongolia, Gansu and Sichuan were separated from the protection system. The main wetland types in the middle reaches of the Yellow River were riverine wetlands, with low protection coverage rate and large conservation gaps. After protection network system being optimized, the protection effect was improved by29.1%-37.6%. The wetland in the lower reaches of the Yellow River was mainly concentrated in the Yellow River Delta area. The protection system was good and the conservation gaps was small. Overall, riverine wetlands in the middle reaches of the Yellow River basin had the highest area proportion of conservation gaps which needed more attention. Based on the priority conservation pattern, our results provided scientific suggestions for the protection planning and management of wetlands in the Yellow River basin, which would lay a foundation for the water ecological protection of the Yellow River basin from the macro scale.