A fully isolated, high-precision synchronous trigger system with MOPA structure of excimer laser was introduced. Firstly, the phase-locked loop phase shift technology combined with the traditional pulse counting method was proposed to realize the high resolution and large range of the system; Secondly, the full electrical isolation way was used to achieve long-term stable operation and real-time control of the system in a complex electromagnetic interference environment. The main parameters of the system reached a resolution of 1 ns, a delay and pulse width adjustment range of 0-325 μs, the jitter between each channel was less than 60 ps, and the front and back edges were less than 1.5 ns. Synchronous trigger system applied to a set of 193 nm deep ultraviolet MOPA structure excimer laser device. It realized the precise real-time control of MOPA dual cavity discharge sequence under the high repetition frequency of 4 kHz, the relative discharge delay can be strictly controlled in the best time period, the discharge timing jitter was less than ±4 ns, and the pulse energy amplification of the MO cavity seed light was successfully obtained by the PA cavity. The magnification rate reached 19.2, and the maximum output pulse energy reached 7.1 mJ. It meets the needs of deep ultraviolet lithography applications.