The safety of safe crop products (SCP) is critical to maintain peoples health and living standard. With the global efforts on the improvement of the traceability of food products, it is inevitable to establish corresponding traceability systems to monitor the safety of crop products in China. In this article, the supply chain pattern of SCP in China has been analyzed and its spatial characters have been described in detail. The study deals with on how to relate traceability technology with GIS, and on how to trace and retrace the safety of SCP using the function of excellent spatial representation, spatial locating, and spatial analysis provided in GIS, which has been discussed from several aspects, such as coding technique of traceability information, transferring technique of traceability information, spatialization of traceability information, and application integration of traceability system. A pilot study was carried out to present the basic functions of the system, which provided an efficient and credible way to trace and retrace the safety of SCP in a real supply chain. An innovative idea has been brought forward for how to establish an efficient, credible, applied traceability system of SCP.