Under network externality, this paper investigates the impact of network externality, competition intensity and market risk on the choice of the vertical control structure of the competitive supply chain, and addresses the evolution process and the equilibrium of the vertical structure from the aspect of manufacturer’s profit and supply chain’s profit. The choice from manufacturers is influenced by the competition intensity and market risk, which are influenced by the network externalities. When the network externality changes, the competition intensity and market risk play different role in the choice of the vertical control structure. The choice from supply chains is irrelevant to the market risk, which is influenced by the network externality.