Combinations of spherical vessels and pipes are frequently employed in industries. Scholars have primarily studied gas explosions in closed vessels and pipes. However, knowledge of combined spherical vessel and pipe systems is limited. Therefore, a flame acceleration simulator was implemented with computational fluid dynamics software and was employed to conduct natural gas explosions in three structures, including a single spherical vessel, a single spherical vessel with a pipe connected to it, and a big spherical vessel connected to a small spherical vessel with a pipe. These simulations reflected physical experiments conducted by at Nanjing Tech University. By changing the sizes of vessels, lengths of pipes, and ignition positions in linked vessels, we obtained relevant laws for the time, pressure, temperature, and concentrations of combustion products. Moreover, the processes of natural gas explosions in different structures were obtained from simulation results. Simulation results agreed strongly with corresponding experimental data, validating the reliability of simulation.