The cross-regional characteristics of e-commerce increase the innovation benefits of micro and small enterprises, but the natural monopoly of e-commerce platform will inhibit the innovation of micro and small enterprises. Based on the data of China Micro and Small Enterprise Survey, this paper empirically tests the impact of e-commerce on the innovation of micro and small enterprises. It is found that : (1) e-commerce can not only promote the innovation of micro and small enterprises in product and technology, but also promote other innovation such as marketing, organization, and service. (2) Micro and small enterprises accelerate the return of capital through developing e-commerce, increase the cash flow, and make it easier to innovate. Increasing investment in advertising of micro and small enterprises through e-commerce platforms can promote other innovation such as organization and marketing, but the promotion effect on product and technology innovation is not significant. (3) Compared with strong competitiveness of main product in the market, enterprises with weak product competitiveness have better effect in using e-commerce to carry out innovation other than product and technology. There is no significant difference in the innovation effect of e-commerce among micro and small enterprises in different regions.