Abstract: Farmers play an essential role in multi-stakeholder collaborative mechanisms for the protection of important agricultural heritage systems. Investigating and evaluating the subjective willingness of farmers to protect agricultural heritage systems is of great significance for guiding the protection and sustainable development of important agricultural heritage systems. However, insufficient farmer participation has caused heritage protection to face various practical challenges, and it is necessary to study the subjective willingness of farmers. Using the analytical framework of farmers’ participation in heritage protection under situational interaction, this study employed the Dike-Pond Agricultural System in Foshan, Guangdong (one of China’s Nationally Important Agricultural Heritage Systems) as an example and adopted the Q methodology for research design. Farmers were invited to rank the Q statements of heritage protection voluntarily after in-depth interviews. The Q-Sorts data were analyzed using the PQ Method 2.35 software, and the cognition, emotion, attitude, and behavior of farmers with different protection intentions were further discussed and compared. The results showed the following: 1) The software extracted four representative factors. Their eigenvalues were 10.334, 4.028, 2.741, and 1.891, and four factors were accepted and interpreted after factor rotation. According to the scores of each statement, farmers’ protection willingness was divided into four types: potential protection willingness oriented, avoidance protection willingness oriented, native protection willingness oriented, and development protection willingness oriented. 2) The willingness of farmers to protect the heritage was closely related to their age, educational background, and work in agriculture. Among them, elderly small-scaled farmers mainly have low protection willingness, while large-scaled farmers were groups with potential protection willingness. 3) There were obvious differences in the three aspects of cognition, attitude, and behavior among farmers with different degrees of willingness to protect. Native protection willingness-oriented and development protection willingness-oriented farmers had a higher awareness of heritage protection than the other farmers, but the difference was that they focused on different protection methods. Avoidance protection willingness-oriented farmers did not pay attention to heritage protection and emphasized the role of the government. Among them, weak cognition and livelihood difficulties were the main reasons for farmers’ low willingness to protect. The innovative aspect of this study was to comprehensively use qualitative and quantitative methods of Q methodology to design research to explore farmers’ willingness to protect from their subjective vocabulary and summarize and analyze different protection willingness types. To increase the willingness of farmers to protect heritage sites and fulfill their role in protecting the Dike-Pond Agricultural System, it is necessary to improve farmers’ understanding of important agricultural heritage systems, strengthen the livelihood guarantees for farmers in heritage areas, stimulate the protection potential of farmers with potential protection willingness, and enhance their ability to participate in heritage protection.