A method and an apparatus for synchronizing a data stream are disclosed. The method includes: decoding the data stream to generate a decoded data stream and program clock references; generating a local clock reference; generating a simulated clock reference according to the program clock references and the local clock reference; comparing the local clock reference with the simulated clock reference to generate a comparison result; adjusting a processing timing of the decoded data stream according to the comparison result; and processing the decoded data stream according to the processing timing.