A control method for error handling in a controller, storage medium therefor, controller, and storage device. The controller for use in a first device is capable of linking to a second device according to an interconnection protocol. The control method includes the following steps: handling a first error information by transmitting a negative acknowledgement control (NAC) message to the second device according to the interconnection protocol through the controller, wherein the first error information indicates a first error occurring while the controller performs data reception according to a protocol layer of the interconnection protocol; and setting error handling status data to indicate that error handling is asserted for the first error information so that the controller does not handle sequence number errors occurring after the first error until the error handling status data is set to indicate that the error handling is de-asserted.