With the deepening of international labor division and accelerated flows of products and factors, ports are playing a significant role in the global logistics network. As the key hub of resources allocation within the whole economic system, ports are supposed to be an increasingly more important breakthrough in terms of enhancing comparative advantage. It is urgent that China should endeavor to improve the efficiency of ports in order to enhance comparative advantage. Therefore, it is important to probe into the key factors affecting the efficiency of China’s ports and the efficiency-enhancing methods accordingly. As a result of the new pattern of international labor division and evolvement of ports functioning, ports’ economic relationship are no longer confined within inside. Accordingly, the concept of port efficiency should not be confined to the functioning efficiency of a port per se. Instead, a new concept system of port efficiency should involve the Operative Efficiency within a port per se, the Network Configuration Efficiency between a port and other ports, and the Radiant Efficiency between a port and its hinderland, namely Port Efficiency I, II and III respectively. These three levels of port efficiency are inseparable, and interact with each other. From this perspective, research on port efficiency will have a strong explanatory power of reality. Based on the above-mentioned concept system, the three levels of efficiencies of China’s main coastal ports are measured and assessed via DEA. It’s found that the efficiency indexes of Yangtze River Delta and Shandong ports, Jin-Ji and Pearl River Delta ports, Southwestern and Liaoning ports, can be respectively regarded as high, medium and low. Among them, only the efficiency of Yangtze River Delta ports has been strengthened level by level, while most of China’s ports, port clusters and port-hinderland are inefficient to some extent. Furthermore, the DEA projection shows that most of China’s ports suffer from inefficiency as a result of input congestion and output deficiency. Such inefficiency stems from X-inefficiency within the ports system per se, which in turn results from the distortion in port’s equity structure, and is closely relevant to several factors, including the overwhelming dominancy of state-owned shares in ports’ equity structure as well as the unicity of resources allocating equities during the economic transition. Therefore, the impediments to the enhancement of port efficiency such as the distortion in equity structure can be resolved via the following countermeasures. Firstly, the equity structure should be diversified rather than singularized, with the predomination of private enterprises in resources allocation. Secondly, a contestable market should be established to ensure the free flows of factors. To this end, it is especially important to eliminate miscellaneous barriers to market for private enterprises. Thirdly, incentive comparability between port enterprises as well as between the governments and enterprises should be ensured with the aim of sustainably enhancing the efficiency of China’s ports.