A server motherboard diagnosis method, system, and related circuit system. A management module of the server motherboard and peripheral devices managed by the management module are capable of being powered by a server power source and a USB port. In response to the management module and the peripheral devices being powered by the USB port, a power supply line of the server power source is isolated, as by: identifying the peripheral devices, in response to the management module and the peripheral devices being powered by the USB port; for each of the identified peripheral devices, initializing the peripheral device, and then shutting down the power supply of the peripheral device; establishing a communication between the management module and a diagnosis host through the USB port; and executing a command in response to the command being received from the diagnosis host.