By introducing the theory of social co-governance into the field of e-commerce intellectual property protection, this paper builds an evolutionary game model among the government, e-commerce platforms, and rights holders, and studies the conditions under the stakeholders form a stable equilibrium state under different constraints. Combined with numerical simulation, the influence of individual factors and factor combinations on the system stability is analyzed. Results shows that: Strictly controlling the action costs and response costs of all parties can enhance their willingness to actively deal with infringement issues; reasonable adjustment of the reward and punishment measures of government supervisory agencies can produce sufficient reverse shock and positive guidance to platform and operators; penalties should be imposed on government supervisory agencies that are not sufficiently supervised; strengthen the construction of the social environment for intellectual property protection, improve the social benefits of actively responding to infringement issues, and increase the sense of acquisition by the government, platforms and rights holders. And it provides certain positive references and suggestions for the government to formulate relevant policies.

China’s E-commerce market is very active. Despite the impact of COVID-19, the market has ushered in major development opportunities. Alongside, the level of intellectual property protection in China is constantly improving. However, there are relatively few studies on intellectual property protection in the field of E-commerce. This study introduces the theory of social cogovernance and explores the construction of China’s E-commerce intellectual property protection system with the participation of collective organizations. Evolutionary game method is applied to model construction. Through numerical simulation, the study analyzes the evolution of E-commerce platform and collective organization strategic choice. The results depict that improving the open space provided by E-commerce platforms for collective organizations and strengthening their public service capabilities can promote the construction of social cogovernance systems. The establishment of reasonable reward and punishment mechanisms can increase cooperation enthusiasm. We also discuss the theoretical and practical implications for governments, E-commerce platforms, and collective organizations, to improve the level of intellectual property protection in E-commerce. This study can provide suggestions for China’s E-commerce intellectual property protection, improve the overall level of intellectual property protection in China, and provide a reference for global E-commerce intellectual property protection.