In order to solve the problems of national and international research and the current situation, the following must be addressed: the research method is more traditional; the research perspective is relatively single; the index construction lacks a theoretical basis; the index selection is more one-sided; the data is only cross-sectional; the financial and talent support is insufficient; the service level of public service facilities is not good; the awareness of cultural preservation and inheritance is insufficient; and the level of management across administrative regions is differentiated. At the same time, to meet the top-level design needs of constructing a rural historical and cultural preservation and inheritance system, the non-oriented, region-wide EBM (Epsilon-Based Measure)-GML (Global-Malmquist) model is constructed under the condition of VRS (Variable Returns to Scale), which includes non-desired outputs. Additionally, an index system for assessing the value of rural preservation and inheritance in China is also constructed. Taking the typical rural area in the Western Liao River Basin of Inner Mongolia as an example, the panel data from 2019 to 2021 are selected for empirical analysis, and the conclusions and countermeasures are as follows: 1. The overall preservation improves year by year, and partly shows high preservation in the southwest and low preservation in the northeast. The advantageous areas should update the preservation and inheritance methods to enhance the driving effect on other areas; other areas should continuously improve the quality and efficiency. 2. The difference between rural areas with the highest and lowest assessed values increases year by year, showing the Matthew effect. It is necessary to realize the policy meaning of the value assessment index system by strengthening the overall preservation, integrating the preservation and inheritance into the rural development of the whole basin, strengthening the overall management, reforming the preservation and inheritance management mode, and improving the management efficiency of rural in the whole basin. 3. Strengthen the technical empowerment and scientific preservation and inheritance. It is necessary to learn the advanced technology concept and transform the technical achievements over time.