The Hani Rice Terraces System is one of the Globally Important Agricultural Heritage System (GIAHS) sites approved by Food and Agriculture Organization (FAO). With the development of modern agriculture and tourism, the terraces face several threats, especially from the agricultural sector. Using Zuofu and Mitian Villages of Jiayin Town (Honghe County, Yunnan Province) as case study, this paper analyzed and compared agricultural planting patterns and management measures based on data obtained from field observations and questioner investigation. Zuofu is a traditional village in Jiayin Town while Mitian is a village greatly influenced by modern culture. The results showed that paddy field accounted for about half of the farmlands in both villages. There were more traditional rice varieties cultivated in Zuofu than in Mitian. Fertilizer usage in both villages was below average, mainly due to the unique irrigation systems and organic fertilizer management. Thirty percent of farmer households used organic fertilizer. However, less crop straws were returned to the soil to improve soil fertility. Pesticide use in both villages was in the normal range while more herbicides were used in Mitian than in Zuofu. As Zuofu had more labor and conducted more traditional agricultural planting pattern, it benefited more from weed control. Main problems for local agriculture included loss of labor and traditional rice varieties, and increased fertilizer and pesticide application. It was recommended that local managers should pay more attention to these problems and take countermeasures to conserve the Terrace System and ensure the sustainable development of local agriculture.