The supply-side structural reform in the agricultural sector is an all-round revolution in the production field，a whole industrial chain revolution in the supply field and a synergy revolution in the reform filed. At present，there are three misunderstandings about the policies for the supply-side structural reform in the agricultural sector. Namely，it is simply believed that the supply-side structural reform in the agricultural sector should mainly focus on solving the supply glut of agricultural products，adjusting and optimizing agricultural structure，and changing the development mode of the agricultural sector. For advancing supply-side structural reform in the agricultural sector and completing established goals and tasks，the key point is to foster new-type agricultural operation bodies，stimulate farmers’ voluntary actions，and boost the development momentum and endogenous power of the agricultural sector and the rural area. Compared with common farmers，the farmers’ cooperatives is more powerful in service ability and the mobilization of resources，and it has access to more market channels. While compared with other new-type agricultural operation bodies like family farms and leading enterprises，the farmers’ cooperatives see closer interest connection with farmers and plays greater role in synergy. Therefore，the government should pursue more innovative policies and provide more privilege and support so as to facilitate standardized and innovative development of the farmers’ cooperatives and make the farmers’ cooperatives play a leading role in supply-side structural reform.