The study of human-water relationship is an important field of social-ecological system research. Identification of farmers' perception of human-water relationship and its influencing factors plays an important role in implementing ecological protection and high-quality development policy in accordance with human requirements in the lower reaches of the Yellow River Basin. However, the existing studies have mostly carried out residents' perception survey and attribution from one or several relationships such as regional water resources, water environment, water culture, etc., but ignore the structural interaction mechanism between human and water. Based on 1651 questionnaires distributed to farmers in 10 counties of Shandong Province in the lower reaches of the Yellow River, after the analysis of confirmatory factors, we finally introduced five latent variables:water resources and ecological relationship, water culture and tourism relationship, residential ecological function, estuarine wetland function, and cultural tourism function, and established a structural equation model. It found that the farmers' understanding of water resources and ecological relationship positively affected their assessment of residential ecological function and estuarine wetland function. The farmers' understanding of the relationship between water culture and tourism had positive impact on their assessment of the ecological function of their residence, the function of estuarine wetland, and the function of cultural tourism. The results revealed the influence mechanism of the function cognition of the human-water system by describing the structure of the human-water relationship based on the perception of farmers, which is helpful to provide decision-making reference for ecological protection and rural revitalization in the lower reaches of the Yellow River Basin.