As both domestic and international development experience of specialized farmers cooperatives indicated, innovation plays a vital role in improving the core competitiveness of specialized farmers cooperatives. With the increasingly obvious trend of integration of economy and science, the innovative activities of inter-discipline and cross-organization become more and more frequent. In order to enhance the competitiveness of specialized farmers cooperatives in domestic and international market, the open innovation mode should be implemented， applying its internal and external advantage to extensive cooperation in the aspects of co-innovation in agriculture products, production technology, service-providing and organization systems. At present, it has important significance to research specialized farmers cooperatives collaborative innovation, since domestic specialized farmers cooperatives collaborative ability is weak and related research is lacking. The framework of collaborative innovation development inside and outside specialized farmers cooperatives could be established based on ″strategy-knowledge-organization″ view. On strategic synergy, partners should maintain value convergence and same goals. With regard to the organizational synergy, partners should put highly attention to the organizational coordination and establish unified specialized farmers cooperatives innovation strategy alliance organization. As for knowledge synergy, partners should keep full communication and build knowledge collaborative platform. This study has Selected 23 specialized farmers cooperatives of three countries in Zhejiang province as case study object with the aim to judge the specialized farmers cooperatives collaborative innovation situation and existing problems inside and outside. Many aspects are thoroughly examined, which includes the willingness of collaborative innovation, organization alliance and method of information communication, method of taking shares for members , number of shareholders and membership, board structure, membership participation of specialized farmers cooperatives development, production costs and benefits, profit distribution, services provided to members and regulation operation. As the research result indicated, 23 specialized farmers cooperatives' synergy innovation strategic willingness is weak, and 95.6 percent of specialized farmers cooperatives dont have the willingness of synergy innovation, 94 percent of members lack of synergy innovation sense. The coordinated target among organizations is low. The more support come from government, the weaker specialized farmers cooperatives innovation is. There is a big heterogeneity between members' goals, the expectation between shareholders and ordinary members is different. Partners dont pay highly attention to cooperation, only one specialized farmers cooperative cooperates with scientific research institutions, the reason is that specialized farmers cooperatives are more concerned how to achieve more subsidy according to policy and ignore the collaborative innovation development. Organization lacks of synergy innovation alliance, the organization structure exist in name only. The communication of organization inside and outside is weak, 100 percent of specialized farmers cooperatives don't participate in making policy, 95 percent of ordinary members are not clear about policy which indicates government support specialized farmers cooperatives. The knowledge platform has little effect, 80 percent of specialized farmers cooperatives will not browse the website, and the publication system of specialized farmers cooperatives internal information has less effect. Some factors will impact specialized farmers cooperatives' strategy, organization and coordination, which includes partner heterogeneity character, organizational structure, potential interest risk and incentive policy, communication, credibility and external regulatory environment. As a conclusion, we should build the collaborative innovation strategic vision both inside and outside the organization , enhance the collaborative innovation objective inside and outside the organization, increase the intensity of specialized farmers cooperatives innovation between organizations, improve the system in terms of organization personnel, equity structure and profit allocation, strengthen the communication between organizations, solidify the system of organization information sharing and enforce official supervision.