Abstract: In order to alleviate the deviation of farmers’ green agricultural production willingness and behavior, based on the questionnaire survey data of 437 farmers’ green agricultural production willingness and behavior in Yunnan Province, a binary Logit model was constructed to analyze the reasons why each variable affects the farmers’ green agricultural production willingness and behavior, and its influencing factors, and further used the ISM model to analyze the internal logical hierarchical relationship of the influencing factors. The results showed that: (1) The willingness of farmers to green agricultural production was generally high, but the actual behavior lags behind the level of willingness, and the deviation rate was as high as 43.5%. (2) The willingness and behavior of green agricultural production were complex, and its six levels played a vital role in farmers’ green agricultural production. (3) The internal logical hierarchical relationship of the influencing factors of deviation was as follows: surface factors (farmers’ green agricultural cognition) directly drove farmers’ green agricultural production willingness and behavior to deviate, and were influenced by intermediate indirect factors (farmers’ agricultural production, farmers’ green agricultural cognition, social policy orientation, risk perception and prediction, education and training), and indirect factors in the middle layer were affected by deep root factors (personal characteristics of farmers). It is necessary to further strengthen the development of agricultural greening to promote the transformation of farmers’ green production willingness into behavior.