The invention relates to a method for enhancing link delay fault tolerance in the time synchronizing process. The method includes the steps that (1) a data packet of the link delay time is generated when the link transmission is computed; (2) within a certain time interval, the link delay is computed in a loop mode; (3) Q check sampling processing is conducted on the computed path delay numerical value. By means of the method, the fault tolerance of the link delay is enhanced according to an IEEE1588 protocol computing link delay method. An embedded program runs in an exchange device, no extra hardware device is needed; the jitter data are obtained effectively and scientifically through the statistical method, the step length of the sampling cycle is adjusted according to the actual conditions, and the check process is shortened, and the check efficiency is improved.