Social enterprises (SE) certification is a process of labeling SE and distinguishing them from other types of organizations. This article centers on the SE certification practices in China’s Mainland, Hong Kong and Taiwan, analyzes their development conditions and compares them in the three areas. The research has found that there are many similarities in certification organizers, essential criteria, SE qualifications, government role, the application of certification results in such areas. Meanwhile, evident differences have also been found, which can be explained from the institutional contexts within which social enterprises grow and the maturity of non-profit sectors in these regions. Through the analysis of SE certification practice in the three areas, this article points out that SE certification practice varies in different institutional contexts, but in general it helps social enterprises to construct a unique and distinct identity so as to better acquire support from the market, government and other entities. At the same time, we should be alert to the “fence effect” when endorsing social enterprises, and avoid setting fine-grained indicators which may bring damage to the diversified ecology of social entrepreneurship.