The negative list of foreign management mode in China’s pilot free trade zones has created a fair competition market legal environment for foreign and domestic enterprises. This kind of management pattern conforms to the new trend of the development of international investment rules, and fits to the reform of the administrative system in China. Under the negative list mode, China’s government regulatory system is facing many challenges in the idea, system and results. Pilot free trade zones are set up to open investment as a starting point and to promote the reform of the government. The government management is featured by transforming from prior approval to in-process regulation, and ultimately the implementation of the fundamental transformation of government functions. Negative list mode should not only focus on the improvement of the negative list by text, but also more important is to establish and complete the system of regulation on in-process and subsequent regulation. On current regulation in the pilot free trade zones, there are still some problems. We should take some effective measures to perfect the system of in-process and subsequent regulation in pilot free trade zones, including transformation of regulatory philosophy of change, perfection of legislation, building information platform, improving the assessment mechanism and supervision of the main aspects of the regulatory body.