The new Water Transport Regulations was put into effect on January 1, 2013, which adjusts and revises certain provisions that no longer consist with the water transport development in China. After the new Regulations came into effect, a series of issues require in-depth study and exploration, such as how to manage the market and establish a reasonable and feasible access and exit mechanism for the shipping market, how to give full play to the self-discipline function of guilds and create a market environment featuring order, clear-cut reward and punishment and effective restriction, and how to apply scientific and efficient dynamic regulation. This study sorts out the problems and weak links in China’s shipping market management after the new Regulations is implemented, examines the management mode suitable for the development of Shanghai shipping market, and proposes policy suggestions for Shanghai to standardize the shipping market environment and realize high-efficiency regulation.