A method and system is disclosed for making timing alignment for a data transmission system, the method comprising providing a reference clock signal with a first frequency to a multiplexer through a phase shifter, generating a multiplexed signal with a second frequency by the multiplexer, wherein the second frequency follows the first frequency and is higher than the first frequency by a predetermined proportion, sending the multiplexed signal to a modulator, and phase shifting the reference clock signal by the phase shifter before the reference clock signal is provided to the multiplexer, wherein a timing of the multiplexed signal at the second frequency level can be adjusted by adjusting a timing of the reference clock signal at the lower first frequency level.