Stable land rights can increase farmers’ expectations regarding the future and encourage their adoption of green production methods, which is an important guarantee for promoting the development of green agriculture development. This paper takes the fertilizer use as an example and systematically investigated the impact of land tenure stability on the green production behavior of heterogeneous farmers based on a field survey data of 349 cotton-planting farmers from Xinjiang, China. Furthermore, this research aims to assess the differential impact of land tenure stability on different risk preferences, organizational forms and ethnic groups. This study is a continuation of previous studies on factors influencing green production behavior. The results show that land transfers have an inhibiting effect on farmers’ green production behavior and this effect is more significant among risk-averse farmers, local farmers and minority nationalities farmers. The land tenure period can promote the green production of farmers and alleviate the restraining effect of land transfers on farmers’ green production behavior. Additionally, farmers of Xinjiang Production and Construction Corps (XPCC) and large-scale households are more inclined to green production. The Chinese Government needs to further promote land transfer to large-scale households, improve the stability of land rights and adopt differentiated policies for heterogeneous farmers to encourage their green production.