A container tracking management method and system comprises an electronic custom seal which is arranged on a container, a handheld operation device, a fixed operation device which is arranged on a sluice crossing, a landmark device which is fastened to the fixed operation device, a computer and a background management center system. The system and method is characterized in that a user buys a seal code from the management center by means of the handheld operation device or the fixed operation device, and after the goods packing is finished, the container door is closed, and the sealing is made through the handheld device, and the seal causes the code and related information to be uploaded to the management center to be activated; after the container reaches the destination, the electronic custom seal of the container is unsealed through the handheld operation device or the fixed operation device after the identity authentication, the management center is informed that the logistic voyage is finished. By adopting the method and system, the visual and transparent tracking and supervision of the container can be achieved, so the special sampling inspection can be made to the risky and dangerous containers which are selected prudently and effectively, which ensures the safety of the container freight transportation and realizes the international anti-terrorism of the container.