The traditional calculation method for a transient process has high accuracy when the pipeline only contains liquid, but when the pipeline contains both gas and liquid the accuracy is greatly reduced. The coupling characteristics of gas–liquid interface movement in hydraulic transient processes are not clear due to the lack of high-precision mathematical model and experimental verification. This paper proposes a novel mathematical model of a gas–liquid pipeline system in a hydropower station based on Preissman’s implicit difference scheme and the method of characteristics. The solving mechanism of the transient process of gas–liquid movement was developed on the gas–liquid interface tracking method. Subsequently, the models proposed in this paper were applied in two typical scenarios of a gas–liquid transient process in a hydropower system, and their accuracy were verified in a field experiment. The comparison results showed that the novel model could accurately capture the movement of the gas–liquid interface, and the average relative error of the characteristic parameter was about 7.2%. Under the load rejection condition, the change speed of characteristic parameters was positively correlated with the pipeline slope. Under the pump failure after low-head startup condition, the maximum pumping discharge was negatively correlated with startup water level and the maximum reversal discharge and speed were positively correlated with the pump failure water level. Compared with the conventional method, the proposed model has advantages in solving the complex transient process coupling gas–liquid. It has potential value in applications such as the safe operation of hydropower stations, the transient process of water diversion projects and in urban pipe network operation.