It is hard to simulate the filling process of empty pipes and draining process of liquid-filled pipes in gravity flowed system with traditional characteristics method, because of the changing position and time of corresponding boundary conditions. In this research, Lattice Boltzmann method, as a new 3D transient simulation method, was used to study the filling and draining transient processes of gravity flowed pipes. Different from the traditional one-dimensional analytical method of a system, the Lattice Boltzmann method, which was based on mesoscopic model, built the lattice model of time-space discrete dynamics in gravity flowed pipes according to the essential feature of fluid microscopic movement. Distribution and movement of the mesoscopic fluid particles obeyed the dynamic statistical law, and the fluid macroscopical motion variables could be obtained by statistically averaging a large number of particles in the flow field. Thus this method could deduce visually the changing liquid levels of the filling and draining processes in pipes, fully filling and draining time, changing flow field in the opening gate valves that were respectively at inlet and outlet, as well as the change curves of pressure and velocity at monitoring points behind the valves. At the same time, traditional 1D calculation of the pipe system was used to be compared with the 3D simulation result and make verification. It is an innovative research orientation to use CFD technology to analyze flow field of pipes in system level, which greatly improves the accuracy of results and visually analyzes the transient process of flow field in key location in system as well.