This paper builds a physical model by using the finite element method on COMSOL simulation platform to simulate the in-line PECVD process. The in-line PECVD simulation model couples the flow field, thermal field, chemical reaction field and plasma field and is verified through experiments. In addition, a new simulation strategy is proposed to solve the problem of dynamic coating silicon nitride film. Through this simulation method, process parameters and structural parameters of the in-line PECVD equipment are optimized. Effects of microwave tube position, microwave shield size, total gas flow, pressure and temperature on main coating reaction region is studied. The results have shown that the position of microwave tube, the total gas flow and temperature have greater influence on the region of reaction zone, the concentration distribution of reactants and the thickness of SiNxHy film. Through optimizing process parameters and structural parameters, the coating rate of SiNxHy film can be increased from 0.0607 nm/s to 0.15 nm/s and the deposition thickness can be increased from 6.78 nm to 15.59 nm. The molar concentration of SiNxHy particles in the reaction region has grown by more than 23.5%. And the relative intensity of reaction field inside PECVD chamber has increased by 1.3-2.3, which is calculated by molar concentration ratio of SiNxHy particles. This paper provides a reference for the optimization of in-line PECVD equipment.