The farmers’ deep participation in the classification of domestic waste plays a crucial role in reducing the amount of waste out of the village from the source, lowering the cost of waste treatment, and realizing the sustainable development of rural waste resocialization, reduction, and harmlessness. This paper aims to identify the key factors and logical structure that influence the farmers’ behavior in classifying domestic waste and provide recommendations for improving it. Based on the Participants’ Intellectual Decision (PID) Model, we constructed a theoretical analysis framework for farmers’ decision-making on domestic waste classification, and the PID model was further extended by combining with the practice of rural domestic waste management in China and proposing the research hypothesis that factors, such as community attributes, rules of operation, the status of the participants, and the situation of external actions, have a significant impact on the farmers’ behavior in classifying domestic waste. Empirical analyses were carried out with the help of the ordered logistic model and the DEMATEL-ISM using 939 research data of farmers in Jiangsu and Gansu provinces of China. The results show the following: (1) classification of domestic waste by farmers in the sample area was predominantly unclassified (34.40%) and two-classified (40.58%); (2) 17 factors, including regional disparity, Party affiliation, organizational support perception, environmental emotions, conscious governance attitudes, trust in village cadres, social reference norms, and expected outcomes, have a significant impact on the farmers’ behavior in classifying domestic waste; (3) trust in village cadres, organizational support perception, and environmental emotion are superficial direct factors; incentive measures, fee level, waste transport situation, difficulty perception, self-consciousness perception, social reference norms, and expected outcomes are middle indirect factors; whether or not it is a demonstration village, Party membership and regional disparity are deep root factors affecting farmers to classify their domestic waste.