In China, the seed industry has fierce competition. The situation of homogeneous management and homogeneous products is serious. A key problem is simple and outmoded marketing channel of seed. It threatens sustainable development of seed enterprises. At present, the two-level distribution channel of seed industry has problems of similarity, low access threshold, and unfair benefit distribution, and thus urgently needs innovation. The innovation of distribution channel is inevitable requirement for promoting reorganization of China’s seed industry and building of new order, is necessary weapon for dealing with trans-national seed industry competition, is essential measure for lifting the overall service level of seed industry, and is also essential means for conforming to stage development of China’s agriculture. The innovation of seed marketing channel should consider changes of future agricultural development, deep-level demand of industrial market and services, sci-tech development level, fair distribution of industrial profit, and differentiated competition. It is recommended that channel innovation should follow the flat principle, have new and unique conception, give full play connection advantage of marginal industry, realize complementary advantages and mutual promotion, strengthen service awareness, combine with agricultural development trend, and seek sci-tech innovation of channel carrier – variety.