Abstract: Currently, most harmless disposal refrigerated vehicles use the global positioning system (GPS) to determine the position of disinfection stations and the transport routes of pigs died of diseases. However, the single navigation and positioning information might be unstable when the vehicle was running in remote mountainous area, the information transfer was not continuous, incomplete and untrue. In order to solve this issue, a monitoring system was designed based on radio frequency identification technology (RFID), Beidou navigation satellite system (BDS) and global positioning system (GPS). This paper makes full use of the BDS/GPS dual-mode receiver, which supports positioning and two-way communication functions. On the one hand, it can solve the problem of positioning information instability that occurs when using a single positioning. On the other hand, when the BDS navigation positioning system data appeared to show a deviation, The GPS positioning data from the WGS-84 coordinate system was converted to the CGCS2000 coordinate system of the BDS positioning system, to achieve the purpose of improving the acquisition accuracy of the transport vehicles location information. GAMIT software was used to calculate the 3D coordinates of the observation point, and it was analyzed for the positioning accuracy of combined navigation and single navigation. Floyd algorithm was combined to optimize transportation routes to search for the shortest transportation distance. The harmless transportation vehicles walking map could be drawn from the positioning information of the BDS/GPS dual-mode receiver. The message communication function of BDS satellite was used instead of GSM short message service to realize remote transmission between harmless transportation vehicles and control center. When pigs died of diseases are transported to fixed-point disinfection station, RFID reader will read the vehicle-mounted RFID active electronic tags to recognize the transport vehicles and the GPRS network will transmit the fixed-point disinfection monitoring data to the monitoring center. Monitoring center uses the ArcGIS map display to carry out the real-time monitoring of vehicle transport routes, and uses text to speech to realize the intelligent deployment and management of transport vehicles. Meanwhile, monitoring center obtains the transport routes of pigs died of diseases and the fixed-point disinfection monitoring information by analyzing the received data. After field test, the positioning accuracy of BDS/GPS dual mode receiver was 55.13% higher than that of BDS satellite positioning, and 52.71% higher than that of GPS satellite positioning. The networks packet losses value of vehicle terminal acquisition system was 0.26%, and the error rate of vehicle identification of the disinfection point was 0.97%. The results showed that the monitoring system met the requirements of the monitoring and management system in mountainous areas, and it ran reliable and stable. The study provides an effective method for a transport vehicle for the harmless treatment of dead pigs, accomplishes the comprehensive supervision and management of transport vehicles for the harmless treatment of dead pigs. This system can also be adopted as a reference to harmless disposal systems for other pigs that die of diseases, it has practical value.