Abstract: An accurate evaluation of comprehensive effectiveness can greatly contribute to promoting human settlements and sustainable development in rural areas. The purpose of this study was to clarify the basic connotation of rural comprehensive effectiveness, in order to obtain the maximum value with the minimum investment in the mining villages in the transition period using the shortage of mineral, land, and environmental resources. The concept of "comprehensive effectiveness" was introduced to establish the evaluation system, where the input indicators were the capital, labor and land, whereas, the output indicators were the economy, society and ecology in the rural areas. The field investigation, super-efficiency DEA, Malmquist index, and obstacle factor were used to analyze the dynamic change and obstacles of rural comprehensive effectiveness in Miaofengshan of Mentougou District, Beijing, China, from 2010 to 2020. The results showed that: 1) There was an increasing trend in the comprehensive effectiveness level, indicating the significant spatial differentiation of rural comprehensive effectiveness. There was a low overall effectiveness level with the distribution pattern of high in the north and south, and low in the middle. The high-value areas were mainly concentrated in Jiangou, Shangweidian, and Longjiazhuang villages, while the low-value areas were mainly distributed in Dingjiatan, Dagou, and Nanzhuang villages. The large lower and lowest comprehensive effectiveness levels were the key villages of primary concern in the process of industrial transformation. 2) The Malmquist index showed that the Total Factor Productivity (TFP) of comprehensive effectiveness was greater than 1, and the mean Technology Change (TC) was less than 1, where the TFP showed an increasing trend, while there was no significant contribution of technological progress to rural comprehensive effectiveness. Among them, more than 50% villages of total factor productivity showed an improvement trend, only 47.06% of which made technological progress in improving comprehensive effectiveness. There were little differences and fluctuations in the change index of pure technical efficiency. More than half of rural pure technical efficiency showed a downward trend, where the technical efficiency change and scale efficiency change were greater than 1 in most rural areas. Three villages with the highest growth rates were Tanchang, Jiangou and Longjiazhuang villages. 3) The obstacle factors of the comprehensive effectiveness were changed from the restriction of rural infrastructure construction to the transformation investment of mining rural enterprises. There were outstanding regional similarity and spatial heterogeneity in the obstacle factors. The main obstacle factors restricting the comprehensive effectiveness of villages were the investment in the transformation and ecological restoration of mining enterprises, proportion of mining land transformation area, per capita area of cultural facilities, and utilization level of abandoned land in mining areas. The research revealed the distribution pattern and obstacle factors of the comprehensive effectiveness of mining villages in the transition period. The finding can provide a strong reference to formulate the promotion strategies of differentiated comprehensive effectiveness.