The invention relates to a clock tracking method and a clock tracking system based on an E1 channel. The clock tracking method based on the E1 channel comprises the following steps of when a synchronous clock device completes initialization, acquiring an effective frequency reference source and an effective time reference source according to a preset frequency source priority sequence and a preset time source priority sequence respectively; when a current clock investigation cycle arrives, acquiring a clock deviation between a local clock and a main clock in the synchronous clock device by computation according to the effective frequency reference source and the effective time reference source; when the clock deviation is more than a corresponding preset deviation threshold, adjusting the frequency and phase of the local clock, and thus obtaining a real-time adjusted value; according to the real-time adjusted value and a preset model fitting parameter, setting punctuality model weight parameters; and tracking the local clock according to a punctuality model weight parameter setting result. According to the method of the invention, the reliability and accuracy of time synchronization of the whole network can be improved.