Disclosed is a multi-machine program flashing system based on CAN buses. The multi-machine program flashing system comprises an electric control module, an indication module, a power source, a controller module, CAN receiving and dispatching modules, USB to CAN tools, a computer, a plurality of switches and the CAN buses. The electric control module and the indication module are connected with a plurality of products in parallel through the switches. The electric control module and the indication module are electrically connected with the power source and the controller module. The power source and the controller module are electrically connected. The controller module is electrically connected with the CAN receiving and dispatching modules at the same time. The CAN receiving and dispatching modules are electrically connected with the USB to CAN tools at the same time. The USB to CAN tools are electrically connected with the computer at the same time; the CAN receiving and dispatching modules are connected with the multiple products through the CAN buses at the same time. The invention further provides a multi-machine program flashing method based on the CAN buses.