In the study of hydroelectric system, the research of its transient process and the improvement of its simulation accuracy are restricted mainly by the precision mismatch among the hydraulic and power system models. Simulink provides a very rich control and automation model library system, thus electrical and mechanical conditioning control systems can be accurately simulated. However, it can only solve time but spatial integral problem. Due to that cause, the hydraulic system model often needs to be simplified in course of the simulation of hydroelectric transient process. Comsol, a partial differential equation (PDEs)-based multi-physics finite element analysis software, can precisely simulate the hydraulic system model. Being developed in the Matlab environment, it also can seamlessly integrate with Simulink. In this paper, based on the individual component model, an integral hydraulic-mechanical-electric system model is established by implementing Comsol code into the Simulink S-Function. This model helps to study the interaction between the hydraulic system and the electric system, and analyze the transients of a hydro plant. Meanwhile the calculation results are compared and analyzed with the general simulation system only by using Simulink.