A multimedia processing system for processing a program stream containing a program clock reference information. The system comprises a clock generator, a timer, a modifier, a processing unit, a parser and a compensator. The clock generator generates a clock signal. The timer receives the clock signal and generates a time information. The modifier incorporates a timing reference information into the program stream, wherein the timing reference information is provided according to the time information and the program clock reference information. The processing unit processes the program stream to generate a data stream incorporated with the timing reference information. The parser extracts the timing reference information from the data stream. And, the compensator generates a control signal according to the timing reference information. Wherein the clock generator receives the control signal and adjusts the clock signal.