The innovation of customs clearance facilitation system is one of the key tasks of Hainan Free Trade Port to realize trade facilitation and rule of law, and it has important practical significance for the development of Hainan Free Trade Port. The main institutional paradigms of current customs clearance facilitation include national customs clearance integration, customs inspection integration, and cross-border e-commerce retail import and export customs clearance. This provides alternative references and specific directions for breakthroughs in the system innovation of Hainan Free Trade Port’s facilitation of customs clearance. The successful customs clearance facilitation system practices of typical foreign free trade ports such as Singapore Port, Rotterdam Port, Dubai Port and Hong Kong, China also provide important enlightenment for the institutional innovation of Hainan Free Trade Port. Hainan Free Trade Port should, on the basis of innovating and perfecting“one-time declaration, stepby-step” customs clearance, uniquely innovate the port area’s customs clearance regulations and policies list publicity system, uniquely innovate the“port + port area”single window system under the command of customs and innovate the system of authorized economic operators in the port area in a distinctive way, so as to push international standard Hainan Free Trade Port customs clearance facilitation system to a new level.