With the developing of the agricultural information, it is inevitable trend of the development of agricultural electronic commercial affairs. On the basis of existing study on the development application model of e-commerce, combined with the character of the agricultural information, compared with the developing model from the theory and reality, a new development model electronic commerce of regional agriculture base on the government is put up, and such key issues as problems of the security applications, payment mode, sharing mechanisms, and legal protection are analyzed, etc. The among coordination mechanism of the region is discussed on, it is significance for regulating the development of agricultural e-commerce and promoting the regional economical development.