In the knowledge economy, the innovation already became the motivation of foundation for organization growth, especially for E-commerce organizations. Business organizations should consider how their organizational innovations for all aspects of resource optimization to increase efficiency. The purpose of this study is to build some conceptual models in transformational leadership, innovation atmosphere and E-commerce organization innovation. Through the questionnaire survey procedure in some E-commerce corporations in Zhe Jiang, this research takes correlation analysis and regression analysis. We discovered: both transformational leadership and innovation atmosphere have the remarkable influence on E-commerce organization innovation. We also find the differences of effects and their interactions directly between the transformational leadership, innovation climate and the dimension degrees on E-commerce organization innovation.