From the perspective of household economy, the application of a multiscale spatial econometric model to realize the objective evaluation of county-level poverty alleviation stability is a core issue in rural economics research. The improvement of economic income and livelihood conditions for small farm holders are significant manifestations of poverty alleviation stability. Quantitative evaluation of the county-level poverty alleviation stability can provide a scientific basis for the adjustment of rural economic policy and high-quality development of regional economy by the multiscale spatial econometric model. This study realizes the quantitative evaluation of county-level poverty alleviation stability by constructing the evaluation index system, taking five counties in China’s Yunnan Province as an example, using the exact 2242 survey datasets, and adopting the multiscale spatial econometric model. The main idea of the model is to obtain the score of poverty alleviation stability by weighted summing of dimensions on the basis of weight calculation of each evaluation index. Results revealed the following: (1) County-level poverty alleviation stability includes the stability of regional poverty alleviation and the stability of farmers’ poverty alleviation, which is mainly affected by the combined effect of five factors, including economic and ability status, cognitive level, supporting facilities, and social governance. (2) Based on the multiscale spatial econometric model, the overall poverty alleviation stability in the five counties is relatively low, with Zhaoyang District showing the highest stability, followed by Yiliang, Yuanyang, Honghe, and Gongshan. (3) Farmers’ poverty alleviation stability in all counties, except Zhaoyang, is higher than that in the region. County-level gross domestic product and fiscal revenue are the dominant factors affecting the stability of poverty alleviation in the region, while the dominant factors affecting the farmers’ poverty alleviation stability are the level of per capita net income and labor force proportion in the household population. (4) To enhance poverty alleviation stability, this study suggested enhancing the level of economic development in counties and strengthening the collective economy of the village, innovating the form of economic development of the village, taking the enhancement of the development capacity of counties, relying on resource advantages to actively develop special industries, and improving the stability and sustainability of income generation for farmers. Meanwhile, we propose to further improve the conditions of regional infrastructure and enhance the capacity of public services. The findings can help enrich the theoretical research system of rural economics, expand the scope of research on small-holder farming systems, and provide a reference for diversification of small farm holders economy, the improvement of agricultural farming technology, and the high-quality development of regional economy in China.