The Honghe Hani Rice Terraces System (HHRTS) is one of the Globally Important Agricultural Heritage Systems (GIAHS) sites approved by Food and Agriculture Organization (FAO) in 2010. In recent years, with the development of modern agriculture and tourism, cultivation practices for high yield and uniform variety cropping, has threatened the stability of the system of forest-village-paddy-rivers in the Hani terraces. From the viewpoint of farming behavior, we carried out our surveys to learn about the local rural households’ planting situations and the factors that influence their planting choices. A Participatory Rural Appraisal (PRA) was used for gaining information in Yuanyang County, Yunnan Province. Seemingly Unrelated Regression (SUR) were used to test the theoretical result at the individual rural household level. Then, this paper summarized the status quo of crop cultivation structures and analyzed their driving factors in HHRTS. The results showed as follows: ① In the 41.23 hm2 available farmland referred in survey, the crops grown, ordered by total cultivated area, are hybrid rice, corn, and fruit, which rank as the top three for all crops. As the regional traditional crop, the cultivated area of red rice is only 12.04% of total available farmland referred to in the survey. ② According to the actual plantation, the rural household is divided into two categories and marked as “the red-rice-plantation-oriented household (RR household)” and “the hybrid-rice-plantation-oriented household (HR household)”. The result of the SUR model showed that the driving factors to plant hybrid rice and red rice varied greatly with different categories of the rural household. ③ Consistent with the results of correlation analyses and factor analyses, significant driving factors of red rice planting included the ethnicity of the household, the average altitude of the farmland, and the labor productivity of red rice. Significant restraint factors included the total number of family members and the yield of red rice per unit area. Thereupon, in order to realize the dynamic protection of HHRTS, we established an encouragement mechanism for improving the proportion of red rice plantings in relation to aspects of the rural household, the community, and the local government.