The invention discloses a method and a system for synchronizing single event list data in positron emission tomography (PET). The method includes that at first, single event list data of each independent working detecting module is obtained, probability density of an occurrence time interval of a single event in each detecting module is calculated, and initial parameters are set; then iteration peak seeking and classification time window peak seeking are used for determining initial detecting time difference values of all detecting modules; and finally the difference values are used for conducting synchronous correction and fitting screening on single event data in each detecting module. The invention further discloses a system for synchronizing the single event list data in the PET. The system comprises a data obtaining and frequency difference compensation module, an initial parameter setting module, a rough time scale fitting module, a fine time scale fitting module and a data synchronization correction and fitting screening module. The method and the system for synchronizing the single event list data in the PET can finish synchronization of the single event list data effectively and accurately, simultaneously complexity of system hardware design is greatly simplified, and flexibility, expansibility and adaptability of the system are improved.