A method and a device for multi-channel data alignment in a transmission system are provided, wherein the method comprises receiving a first stream data and a second stream data, determining a deleting/inserting state of the first stream data and the second stream data to generate an information of mismatch data due to a speed difference situation, generating a reverse inserting control signal or a reverse deleting control signal to completely restore the original first stream data and/or the original second stream data at a transmission end, deleting/inserting the first stream data and the second stream data simultaneously after receiving the deleting/inserting state of the first stream data and the second stream data, and outputting the corrected first stream data and the corrected second stream data without mismatching.