A command processing method and a storage controller are provided. The command processing method includes: receiving multiple read-modify-write (RMW) commands by a command processing pool of the storage controller, wherein each of the RMW commands includes a read command and a write command in pairs; locking a queue by the command processing pool and transmitting a pending first read command of the RMW commands in the command processing pool to the queue; when a second read command paired with a second write command of the RMW commands is pending, not locking the queue by the command processing pool and not transmitting the second write command to the queue; and when a third read command paired with a third write command of the RMW commands is not pending, locking the queue by the command processing pool and transmitting the third write command to the queue.