The invention provides a power-down protection system applied to a server, a method and the server. The system comprises a server main board, a CBB control board, a sas control board, a CMC hard diskboard, a power supply battery, a storage device and at least two hard disk connection expanders. A BMC chip of that motherboard is connected with an external power supply through a power supply module, so that the external power supply supplies power to the server. A memory, a power supply battery, a memory, a sas control board and a CMC hard disk board are respectively connected with a BMC chip of that CBB control board. When the BMC chip detects that the server is powered down, it immediately starts the power supply battery and writes the data in the memory of the server into the built-in storage during the power supply battery. When the server is powered on again, the data in the storage is restored to the memory, which protects the data effectively.