Currently, the effectiveness of construction of pilots for Cross-border Data Flow in Free Trade Zones (Port) of China is mainly reflected in model innovation and technological innovation, and the institutional innovation has achieved little effect. With the establishment and improvement of the legal system for the governance of cross-border data flow at the national level, and the unification of the authority of the competent authorities, it is timely for the free trade zone (free trade port) to carry out relevant institutional innovation.This paper holds that free trade zones (port) to carry out the relevant institutional innovation should follow three basic principles: more emphasis on“development objectives”on the basis of taking into account“security objectives”; more attention should be paid to promoting the implementation of relevant regulatory systems on the basis of clarifying the boundary of the approval power; more attention should be paid to summarizing and refining Chinese governance programs of data flows on the basis of insight into international trends. Considering this, this paper suggests that the institutional innovation of cross-border data flow in free trade zones (port) can be launched around five core points: to assist the smooth landing of the data exit security assessment mechanism, first explore the personal information protection and certification mechanism, optimize the standard contract in line with the trade situation, promote the transparency of the data exit evaluation standards, and facilitate the processing of the high-frequency exit of the same subject data.