The innovation ecosystem is based on self-organized evolution, and its theoretical supporters believe that all-win achievement is the inevitable result of system evolution, but recent studies have challenged the conclusion and show that innovation ecosystem may evolve to a failed status. At present, there is a lack of systematic theory support and test of this issue. Previous studies of innovation ecosystem have suggested that focus firms are the determinant factors affecting system evolution, and neglect the effects of firm cooperative attitudes or participation motivation on system evolution. In fact, firms' cooperative behavior also shows the resource dependence relationship to carry out cooperative innovation of bodies with equal status. Based on evolutionary game model, this paper analyzes the self-organized evolutionary process of cooperative innovation between focus firms and supporting enterprise communities in innovation ecosystem through resource dependence relationship. Taking participation motivation for cooperative innovation into account, it divides firm behavior into reciprocal cooperation and opportunistic cooperation strategies, and explores the evolutionary mechanism of innovation ecosystem by combining with technology spillover, cooperative contract etc. Through model analysis and numerical simulation, it comes to the conclusions as follows:firstly, cooperative attitude or participation motivation affect the efficiency and trend of system evolution; secondly, when the increase in losses of technology spillover is harmful to the formation of stable cooperative relationship among firms, and firms tend to select the opportunistic cooperation strategy, leading to the system evolution toward low efficiency; thirdly, the rise in penalties for breaches of cooperative contracts or the increase in innovation capital input are beneficial to the promotion of cooperative innovation among firms, and firms tend to select the reciprocal cooperation strategy, leading to the system evolution toward complete cooperation and all-win achievement. This paper introduces the perspective of resource dependence relationship cooperation, gives a preliminary explanation of self-organized evolution mechanism of innovation ecosystem, and thereby provides theoretical support for firm innovation decisions and the governance of innovation ecosystem.