Abstract: Animal husbandry is an important pillar industry related to the national economy and people’s livelihood. Promoting the green development of animal husbandry is the focus and main direction of the future supply-side structural reform of agriculture and animal husbandry, high-quality development of agriculture and animal husbandry, and rural revitalization strategies. Under the background of the implementation of the new round of grassland compensation policy, based on the survey data of 277 herdsmen in Zhaosu County, Xinjiang, the Logistic-ISM model was used to explore the significant factors affecting herdsmen’s green production willingness and behavioral deviation, as well as the correlation and hierarchical structure of the factors. The results showed that 57% of the sample herdsmen’s green production intentions and behaviors were diverged. Factors such as gender, education level, grassland size, animal husbandry income, recognition of grassland reward policy, economic benefit recognition, technology availability, subsidies distribution timeliness and animal husbandry ecological infrastructure had a significant impact on herdsmen’s green production willingness and behavioral deviation. After further analysis of the logical hierarchy among the influencing factors, it was found that gender, education level, grassland size and subsidy distribution timeliness were the most important deep root factors, animal husbandry income and technology availability were the indirect factors at the middle level, while the recognition of grassland compensation policy, economic benefit and animal husbandry ecological infrastructure were the direct factors at the surface. On this basis, it is proposed to strengthen policy publicity and support, enhance the green production awareness of herdsmen, and stimulate the endogenous power of herdsmen’s green production, strengthen green technology support and provide professional technical guidance, improve animal husbandry supporting facilities and improve external constraints, so as to promote the conversion of green production intentions of herdsmen into actual behaviors, and realize the goal of green animal husbandry and green high-quality development of animal husbandry.