This paper explored how rural cooperatives influence technology efficiency of farmer in the context of Geographical Indication (GI) products industry and identify the main influence factors, to realize regional sustainable development. Based on a survey of rural households in Qingyuan County located in the northeast forest zone in China, where is famous for GI product - Chinese Gentian (a Chinese herbal medicine), the efficiency enhancement mechanism of two groups of farmers (cooperative participants and cooperative non-participants) is analyzed, a meta-frontier analysis (MFA) model is constructed to empirical analyze the impact of farmers' participation in cooperatives on the efficiency of Chinese herbal medicine cultivation, and the heterogeneity of farmers that influence technical inefficiency is identified. The conclusions include: Two different ways to participate in the cultivation of GI products are through cooperatives and self-participation which keep farmers at different frontiers of production; The difference in efficiency within the rural cooperative is small but the efficiency of self-participating farmers is relatively large; The efficiency is about 32% higher, which explains the main reason for increase the efficiency of farmers are unified management, skill training and knowledge information diffusion. Household head age, education, enthusiasm and agricultural skill are the main influencing factors of technology inefficiency. This paper enriches the understanding of how rural cooperatives promote technology efficiency of rural households, especially with the heterogeneity of farmers' endowment, and how this contribute to the adaptive management of local GI brand and targeted poverty alleviation to realize rural revitalization.