A command processing method and a storage controller are provided. The command processing method is adapted for the storage controller. The storage controller includes a processor and peripherals. The command processing method includes: disposing a first command buffer and a second command buffer in the processor; disposing a synchronizer in the storage controller, the synchronizer changing a value of a flag at a predetermined interval to set the first command buffer or the second command buffer valid; and when the first command buffer is valid and the processor issues a command, the processor temporarily stores the command in the first command buffer and one of the peripherals accesses the command in the first command buffer to executes a corresponding operation.