Big data-based price discrimination, as a social phenomenon, has found its social expression more and more frequently. The government, as the main body of market supervision, plays an important role in the governance of this practice. In view of an exploration of the selection and influence of the government’s regulatory strategy in this kind of price discrimination, a research has been conducted on the evolutionary stability strategy of both e-commerce company and government by constructing an evolutionary game model. Research shows that, with the benefits obtained by the government less than the cost, the evolutionary stability strategy tend to be a loose supervision, otherwise, there is no evolutionary stability strategy; long-term strict regulation can inhibit e-commerce enterprise’s big data-based price discrimination behavior, but it also requires long-term consumption of government funds, therefore it is suggested that the government should set up special funds for this expenditure; the stronger the initial willingness of government to implement the strict supervision strategy, the slower the strategy will evolve into a big data-based price discrimination.