A control system for a storage apparatus includes two input/output modules (IOMs), and two non-volatile memory (NVM) devices that are electrically connected to the IOMs, respectively, and that each store a firmware code. Each of the IOMs is configured to execute a firmware corresponding to the firmware code stored in the corresponding NVM device, and to enter an active mode or a passive mode after executing the firmware. The IOMs are configured such that when one IOM operating in the passive mode detects abnormal operation of the other IOM operating in the active mode, the one IOM sends, to the other IOM, the firmware code stored in the NVM device electrically connected to the one IOM, in order to update the firmware code in the NVM device electrically connected to the other IOM.