Abstract: Farmland protection in China faces huge challenges, and the quantity and quality control of cultivated land is a fundamental prerequisite for protection. At the same time, to promote the sustainable development of agriculture in China, it is necessary to enhance the resilience of agricultural ecosystems. Therefore, from the perspective of natural value, it is important to explore the identification and spatial distribution of high natural-value farmland. This article drew on researches into farmland protection by many scholars, introduced the concept of high natural-value farmland, and explored the role of high natural-value farmland in the construction of China’s farmland ecosystem. Taking Yunnan Province as an example, ArcGIS and InVEST models were used for quantitative analysis as an identification method for exploring high natural-value farmland in Southwest China. It used four sets of land use data in 2009, 2012, 2015, and 2018 to calculate the quality of farmland habitat in each year, and the spatial distribution patterns of high natural-value farmland in each year were studied. The main conclusions were as follows. 1) According to existing literature, it was concluded that high natural-value farmland was mainly divided into the following three types: ① farmland with a high proportion of semi-natural vegetation; ② farmland with low-intensity agriculture or small-scale semi-natural farmland mosaic; and ③ farmland for maintaining the survival of rare species. At the same time, high natural-value farmland is ecologically fragile and usually presents a small-scale mosaic form. 2) According to the evaluation results, from the perspective of the time pattern, the proportion of high natural-value farmland changed little from year to year, with an average of 10.86%, mainly small patches adjacent to forest land and water. Farmland with a low natural-value accounted for the largest proportion (82.43%). It was widely distributed in Yunnan Province and had a high production value. This showed that the “ecological-production” value of farmland in Yunnan Province varied considerably. The production value of concentrated contiguous areas was high, but the natural value was low, while the production value of small plots adjacent to forest land and relatively fragmented waters was low, but the natural value was high. 3) From the perspective of spatial pattern, the natural value of farmland in Yunnan Province is generally low; moreover, the proportion of farmland with high natural value is relatively low. It is distributed in parts of northwestern and northeastern Yunnan. The patches are fragmented and scattered around the contiguous farmland. Otherwise, there are two groups of factors that affect the distribution of high natural-value farmland. One group includes human factors: economic growth, urban development, and environmental pollution. The second group includes natural factors: topography, changes in precipitation, temperature distribution, and vegetation cover. Finally, the study analyzed farmland ecosystem biodiversity and agricultural cultural heritage protections from the perspective of natural resources. We proposed policies for farmland protection at different levels or returning farmland to forests, thus realizing the protection concept of “co-governance and joint construction, and the same management and protection.”