A data storage system includes a controller comprising pipelined multiple processors. The controller is configured to: generate plural instructions having dependency based on a command, input from an external device, for controlling at least one storage device to perform an operation corresponding to the command; allocate the plural instructions to the pipelined multiple processors in stages; and reallocate, when a number of second instructions allocated to a second processor of the pipelined multiple processors becomes a first threshold or greater, at least one of the second instructions to a first processor of the multiple processors.