A method for error handling of an interconnection protocol, a controller, and a storage device are provided. The method includes receiving a frame error position indication signal to indicate whether an error occurs in a frame in each clock cycle and a symbol position corresponding to the error, and receiving a frame correction position indication signal to indicate whether the frame in each clock cycle is correct and a symbol position corresponding to the frame that is correct; according to the frame error position indication signal and the frame correction position indication signal, determining that a frame error occurs in a first clock cycle, and after requesting for NAC frame transmission, sending a request for disabling the NAC frame transmission; and after the first clock cycle, comparing the frame error position indication signal and the frame correction position indication signal.