A 3D model coupled with the Volume of Fluid (VOF) method of water-air two-phase flow is applied, and the roughness of walls is considered. The water-air two-phase flow simulation of the covered culvert is carried out while Jinan section of first-phase in east line of south-to-north water diversion project is taken as a case. The flow field of inverted siphon is discussed. The flow of inlet and outlet transition sections is gentle; the velocity distribution is nonuniform and the pressure distribution shows layered on current cross section. The water depth along the channel is downward.