By analyzing the connotation of the adaptability of rural production space system, and constructing a framework of the adaptability, this research establishes an evaluation index system for the space system in the following three dimensions: the vulnerability, the stability, and the response. Then, taking Jiangjin district of Chongqing as an example and using the adaptive evaluation model, this paper evaluates the operation status of the rural production space system from 2007 to 2017. At the same time, the factors of the adaptability obstacle of rural production space system were diagnosed by using the obstacle degree analysis model, and the indexes of the adaptability of rural production space system and the adaptability obstacle degree of criterion layer were calculated. Based on the above research, by analyzing the factors that cause the obstacle to the adaptability of the rural production space system, this paper puts forward some targeted strategies to solve the current reality of the dilemma in the operation of the rural production space system in Jiangjin district of Chongqing. The results show the following aspects. From 2007 to 2017, there is a trend of rising and increasing volatility of the adaptability of rural production space system in the study area on the whole, which shows that the sustainable operation and development capacity of the rural production space system has been improved steadily. The degree of adaptability obstacle of rural production space system has gradually changed from stability obstacle and responsiveness obstacle to vulnerability obstacle, and the key obstacles of the adaptability of the system include the amount of fertilizer used, the amount of agricultural film used, the total energy consumption of rural production, the area of urban industrial and mining land, and the proportion of rural environmental protection investment. It is the key to enhance and improve the adaptability of rural production space system in the district, which aims, on the premise of developing ecological agriculture and organic agriculture and strengthening environmental protection, to reduce the vulnerability of the system, expand the value-added space of selenium-enriched agriculture, effectively increase rural investment in capital, talent and technology to strengthen the stability and response ability.