As an important part of farmland, the slope farmland is widely distributed in the central and western plateau mountain region in China. It is necessary to scientifically evaluate the slope farmland quality (SFQ) and analyze the spatial structure characteristics of SFQ to ensure reasonable utilization and partition protection of slope farmland resources. This paper takes the typical plateau mountain region—Yunnan Province in China—as an example and systematically identifies the leading factors of SFQ. The sloping integrated fertility index (SIFI) is adopted to reflect the SFQ. The evaluation system is built to quantitatively evaluate the SFQ and the spatial structure characteristics of SFQ were analyzed by a geostatistical model, autocorrelation analysis and spatial cold–hot spot analysis. The results show that the SFQ indexes in Yunnan Province are between 0.36 and 0.81, with a mean of 0.59. The SFQ grade is based on sixth-class, fifth-class, seventh-class and fourth-class land. The SFQ indexes present a normal spatial distribution, and the Gaussian model fits well with the semi-variance function of the spatial distribution of SFQ indexes. Furthermore, the spatial distribution of SFQ indexes is moderately autocorrelated. The structural factors play a major role in the spatial heterogeneity of SFQ indexes, but the influence of random factors should not be ignored. The spatial distribution of SFQ grades has a significant spatial aggregation characteristic, and the types of local indicators of spatial association (LISA) are based on high–high (HH) aggregation and low–low (LL) aggregation. The cold spot and hot spot distributions of SFQ grades display the significant spatial difference. The hot spot area is mainly distributed in Central Yunnan and the Southern Fringe, while the cold spot area mainly distributes in the Northeastern Yunnan, Northwestern Yunnan and Southwestern Yunnan. This study could provide a scientific basis for SFQ management and ecological environment protection in the plateau mountain region.