Honghe Hani Rice Terraces System is one of the Globally Important Agricultural Heritage Systems (GIAHS) sites approved by Food and Agriculture Organization (FAO) in 2010. The system of forest-village-paddy-river in Hani terrace, which has formed over 1 300 years in history, has multiple values, including ecological value, economic value and cultural value. However, in recent years, with the development of modern agriculture and tourism, the cultivation practices for high yield and uniform variety cropping bring in serious problems there, such as ecological problems and food security problems. From the viewpoint of farming behavior, we conducted our surveys to learn about the local crop economic input-output, cultivated land resource, rural household information and local natural resources. Participatory Rural Appraisal (PRA) was used to gain the information in Yuanyang County, Yunnan Province. And Seemingly Unrelated Regression (SUR) was used to test the theoretical result on the individual peasant household level. Then, this paper summarized the status quo of crop cultivation structures and analyzed their driving factors in Hani terraces fields. The results showed as follows: 1) In the 41.23 hm2 available cultivated land referred in survey, the plants ordered by their total cultivated area are hybrid rice, maize and fruit, which rank top three in all corps. As the regional traditional crop, the cultivated area of the terrace red rice takes only 12.04% of total available cultivated land referred in survey. 2) The local rural farmer prefer hybrid rice to the terrace red rice due to its much higher economic benefits. Thus, there were more cultivate areas for hybrid rice compared to the terrace red rice. In addition, the terrace red rice is mainly cultivated in the land with poor situation, such as low quality and high altitude. Furthermore, maize is also widely cultivated there for both food and feed. 3）The economic benefit of crop, the quality and altitude of arable land have great influence on the choice of alternative crops, such as hybrid rice and red rice. As for individual peasant household, their characteristics and resource endowment have influence on choosing different corps. The family population and the altitude of cultivated land are positively correlated with the behavior of planting the terrace red rice at the 1% significance level, while the number of cooperatives is negatively correlated with the behavior of planting the terrace red rice at the 1% significance level. The conclusions of this paper is that the decrease of the traditional crop is becoming a trend in Hani terrace fields, especially for individual peasant household. If things continue in this way, it would threaten the stability and sustainability of Honghe Hani Rice Terraces System.