The invention provides a system and method for detecting clock frequency offset of fan chip. The system comprises a fan chip and a control unit. A target pulse width is defined in the fan chip and the control unit. When the control unit executes a detection process of clock frequency offset for the fan chip, it will generate a specific pattern pulse signal and send the specific pattern pulse signal to the fan chip. The fan chip enters a detection mode of clock frequency offset according to the specific pattern pulse signal, generates a response signal including an actual target pulse width based on referring to the defined target pulse width, and send the response signal to the control unit. The control unit compares a difference between the actual target pulse width and the defined target pulse width to detect a clock frequency offset value of the fan chip.