The green transformation of production modes plays an essential role in the sustainable development of China’s agriculture and the modernization process, but there is often a deviation between farmers’ behavior and their willingness regarding green production. This paper analyzed the factors influencing the deviation of farmers’ green production behaviors from their willingness, along with their hierarchical logic structure, using the ordered logit model and ISM model with field survey data of 436 households in Hainan Province. The results show that: (1) there are deviations between farmers’ green production behavior and willingness; (2) age, number of dependents, peer influence, and social networks aggravate farmers’ green production behavior–willingness deviation, while ethnicity, education, land fragmentation, agricultural expenditure, land transfer, neighborhood learning, and green production cognition mitigate the deviation; (3) among the significant influencing factors, farmers’ perceptions of green production, peer influence, land transfer, and agricultural expenditure are the direct surface factors, while neighborhood learning, land fragmentation, and number of dependents are the middle indirect factors, and farmers’ education, social networks, age, and ethnicity are the deep-rooted factors. This study sheds more light and detail on the understanding of the factors influencing farmers’ green production behavior–willingness deviation, and provides more practical and relevant guidance for the agricultural green development in tropical China.