Abstract: Marketization of rural idle homesteads can be promoted for “three rights separation” of rural homesteads. The perceived risk can be one of the most important identification factors in the farmers’ homestead marketization in the reform of the homestead system. In this study, an evaluation system was constructed to identify the risk of homestead marketization from the perspective of farmers’ risk perception, including the risk of the farmers’ equity, cultivated land protection, collective return, social stability, ecological environment, and cultural inheritance risk. Taking Chongqing Dazu, Yongchuan, and other typical homestead system reform pilots as empirical areas, a Variable Fuzzy set was adopted to evaluate the risk level of farmers’ homestead marketization. Subsequently, an efficient machine learning model (called Random Forest, RF) was employed to identify the risk of farmers’ homestead marketization. Finally, risk prevention and control strategies were proposed under different marketization patterns. The results showed that: 1) An inverted “U” shaped fluctuation trend was found in the risk level of farmers’ homestead marketization. Specifically, the risk probability of direct marketization (43.38%) and green indicators marketization (32.14%) were significantly higher than that of marketization of reclamation indicators (13.73%), and marketization of planning adjustment (12.99%). 2) There were some differences in the various risk factors for the four types of marketization patterns. The farmers’ equity risk (46.74%) was higher in the direct marketization, whereas, the cultural inheritance risk (4.76%) was lower. The social stability risk (35.66%) was higher in the marketization of planning adjustment, while the ecological environment risk (5.85%) was lower. The cultivated land protection risk (29.13%) was higher in the marketization of reclamation indicators, while the collective return risk (2.05%) was lower. The farmers’ equity risk (34.24%) was higher in the green indicators marketization, while the ecological environment risk (1.20%) was lower. 3) There were some differences in the risk mechanism. The same risk factor also shared the heterogeneity in the homestead marketization of four types. 4) The differentiated prevention strategies of marketization risks were considered the timing, and the cooperation of various participants, such as farmers, collectives, and governments. The government, the collective, and the farmer were united to focus on the “prevention in advance” in the direct marketization. The collective was supposed to focus on the “prevention in advance” in the marketization of planning adjustment, while the government was on the “prevention afterward”. By contrast, the government was supposed to focus on the “prevention in the event” in the marketization of reclamation indicators, while the collective was on the “prevention afterward”. Only the government was supposed to focus on the “prevention in advance” in the green indicators marketization. In conclusion, the reform of homestead marketization should set the tone of “steady and prudent promotion”. It was different from the complete marketization of state-owned land. But the marketization was limited using “three rights separation”. Meanwhile, future homestead marketization should avoid homogenization patterns. More importantly, it is urgent to establish an income distribution mechanism and risk aversion system, in order to share the benefits and risks by farmers, collectives, and governments. The findings can provide the decision-making on rural residential land consolidation. The homestead risk database can be expected to deepen the reform of the homestead system.