Abstract: With the adjustment of China's economic structure, the problem of related labor relationship is increasingly prominent, and it also challenges China's labor legal system. The traditional labor legislation in China is mainly for the single enterprise labor relationship, rarely involving the protection of the employees in affiliated enterprises. The lack of legislation directly led to confusion in the judicial processing of this kind of labor dispute. We should adopt "Enterprise Entity Theory", and affiliated enterprises will be regarded as a single enterprise as a whole in external relationship. Under the guidance of the theory, we should respond to the common problems of employee protection in affiliated enterprises respectively, and offer reference for the perfection of labor legal system in China.