Yunnan is a typical mountainous province in western China. Its flatland area with a terrain gradient of less than 8° accounts for about 6% of its total land area. A reasonable division of mountainous county, semi-mountainous county and flatland county is an important basic research task, which received considerable concerns from relevant departments and scientific and technological circles of Yunnan Province, for it's the basic foundation for industrial location (especially the location of agricultural production) and cultivated land resources protection in plain area. By using the verified result of the investigation of the flatlands area ≥ 1 km² in various counties (cities, districts) of Yunnan during the Second National Land Survey, selecting three single indicators, including proportion of farmland in flatland area, flatland area proportion, and number of the flatlands with an area ≥ 100 km², and constructing the comprehensive index of Comprehensive Index in Flatland Area (CIFA), and then adopting the method of combining leading indicators with comprehensive analysis, we divide the 129 counties (cities, districts) of the whole province into flatland counties, semi-mountainous and semiflatland counties, and mountainous counties. The division procedure can be separated into three steps: 1) Preliminary classification based on the leading indicators of CIFA; 2) proper adjustment according to the indicators as proportion of farmland in flatland area and flatland area proportion; and 3) adjustment again in accordance with indicator of number of the flatlands with the area ≥100 km². The result shows that there are 21 flatland counties, 37 semi-mountainous and semiflatland counties, and 71 mountainous counties in Yunnan. This study revises Yunnan's previous plan to divide the counties into flatland counties, semi-mountainous and semiflatland counties and mountainous counties by relying solely on one indicator—proportion of farmland in flatland area. It offers scientific foundation and basic support to Yunnan Province and all places throughout the province for them to make rational industrial layout (especially agricultural production layout), and protect high-quality farmland resources in flatland areas.