This study proposes a numerical solution to simulate the transient flow with column separation in pipelines using the lattice Boltzmann method (LBM). By combining the LBM and the discrete vapour cavity model (DVCM), the governing equations and boundary conditions were analysed and derived for numerical simulation. Experiments and actual projects were adopted to verify and examine the new solution. The results indicate that the computational grid of the LBM-DVCM is unrelated to the wave speed, which significantly reduces computational resources and time. Moreover, compared to the method of characteristics (MOC)-DVCM, the LBM-DVCM eliminates virtual pressure peaks during the transient flow. Finally, the LBM-DVCM can simulate the process of transient flow quickly and accurately. It is expected that this method will be useful for practical numerical experimentation and efficient prediction of the pipeline.