With the development of ship intelligence, the frequency of upgrading the marine engine room simulator, which is essential for crew training, has increased. Traditionally, the data processing unit (DPU) of the marine engine room simulator is upgraded by manually downloading the firmware. This makes the hardware maintenance high-cost. In this paper, we first propose a WAN-based firmware upgrade system to enable secure over-the-air upgrades of DPUs and reduce operation and maintenance costs. A distributed hardware structure is given to manage DPU in the simulator via the Internet. We have designed two methods of firmware upgrades, automatic upgrades and remote upgrades. In automatic upgrades, the DPU can download new firmware upgrades from the web server through the router. By designing a series of mechanisms including code rollback, code backup and code confirmation, the In-Application Programming (IAP) technique is realized through the Internet. Firmware upgrades have good fault tolerance mechanisms to ensure that the emulator can still work in the event of an upgrade error. In remote upgrades, we upgrade the DPU firmware through the remote control center. We assessed the performance of the system by measuring the success rate of DPU upgrades, upgrade time and performance after the upgrade. The results show that the DPU upgrade success rate is close to 100% and performance is as good as expected. The results show that the remote firmware upgrade system proposed in this paper is reliable and practical.