It is of great significance to scientifically evaluate the risk level of rural production space system, reveal the characteristics of its spatial pattern, and design risk control measures differently, so as to guide and regulate the multi-subject behavior choice in rural production space system and implement healthy and sustainable rural revitalization strategy. Based on sorting out the risk mechanism of rural production space system, this paper constructs a comprehensive risk evaluation index system of rural production space system from three aspects: the pressure of risk source, the status of risk carrier, and the response of risk control mechanism. Taking 37 districts in Chongqing Municipality as the research unit, and the year 2016 as the time point for the research, this paper evaluates the risk level of the rural production space system and reveals its space differentiation characteristics. On the basis of risk control, we identify the differentiation of rural production space system. The results show that: (1) The generation of risk in rural production space system is the result of interrelation and joint action of risk source pressure, risk carrier status and risk control mechanism response. (2) The risk of rural production space system in Chongqing is generally at a medium level, showing a spatial pattern of "high in the east and low in the west". There are obvious spatial differentiation features of system pressure, status and response level. Finally, differentiated risk control measures are proposed on the dimensions of space control, land use pattern and disaster prevention, reduction and relief system.