Abstract:  Farmers’ professional cooperativeis theproduct of the institutional innovation for achieving various economic goals,especially the potential “exterior profits”. However, there existing low efficiency in farmers’ professional cooperative in reality. From the perspective of the New Institutional Economics, this paper compares the generation mechanisms and operational performance of two tobacco cooperatives. Then analysis results shows that the establishment of two tobacco cooperatives are the institutional changes induced by external profits. Their operation performancedisplaythe obvious difference due to the consent agreement of the main body of institutional innovation can be whether reached. And the policy meaning were put forward to improve the cooperative efficiency in this paper, which is that the preference and benefit coupling mechanism of participants should be taken into account in the design of the institution.