Pressure compensating (PC) emitters exhibit excellent performance in maintaining a constant flow rate over a wide range of working pressures, which are widely used in agricultural irrigation. However, the compensation mechanism of PC emittters is still not clear, which causes huge obstacle in designing and optimizing the structure of PC emitters. To explore the flow restriction mechanism of the PC emitter, the interaction between the elastic diaphragm of the PC emitter and the fluid was investigated by fluid-structure interaction (FSI) numerical simulation method. The deformation characteristics of elastic diaphragm, the dynamic change process of flow resistance and the flow rate of the PC emitter were analyzed. The results indicated that the average error of flow rate between numerical simulation and experiment was 12.32%, which verified the correctness of the numerical simulation. The deformation process of an elastic diaphragm during the entire working process could be divided into three phases: rapid deformation, slow deformation and long-term tiny deformation. With the deformation degree of the elastic diaphragm increasing, the proportion of pressure loss in the labyrinth channel was gradually decreased, while the pressure loss in the PC chamber and overflow groove was significantly increased. The flow resistance mainly occurred in the labyrinth channel, PC chamber and overflow groove. Before the diaphragm contacted convex land, the flow resistance was determined by the capacity of energy consumption of the labyrinth channel, the flow rate of the PC emitter was increased as working pressure was increased. After the diaphragm contacted convex land, the flow resistance and working pressure showed a linear function relationship, the flow rate remained comparatively constant over a wide range of working pressures. Labyrinth channel structure affected the minimum compensation pressure of the PC emitter, overflow groove structure had an important influence on flow rate regulation of the PC emitter. Overall, the research result can provide a basis for formulating a reasonable design method of PC emitters.