The invention discloses a port cold chain transportation system. Automation and thermal insulation during a whole journey of transportation are achieved, the work efficiency is improved, and the coolness and the freshness of goods can be ensured. The technical scheme is as follows: the port cold chain transportation system comprises a goods shelf, an in-cabin traveling device, a goods shelf transporter, a horizontal transferring device, a hatch-cover type transferring platform, a lifting platform, an on-shore loading and unloading crane, a deck loading and unloading hanging beam, a deck loader, a loading and unloading frame, a roll-on roll-off platform, a cold chain transport truck and a thermal insulation cover, and through the combination of the above devices and structures, the complete port cold chain transportation system is formed, so that the goods are automatically taken out of a cabin in each transport link, transported to the shore, pushed into the cold chain transport truck, or taken out of the cold chain transport truck, and transported into the cabin of a cold chain transport ship; besides, automation and thermal insulation during the whole journey of the transportation are achieved.