As the demand for gas increases, the natural gas pipeline network is becoming more and more complicated, and the computational resources and time consumed by pipeline network simulation are also increasing. For the large algebraic equations in the pipeline network simulation, this paper proposes a layered calculation method, combined with the topological structure characteristics of the natural gas pipeline network. This method decomposes the pipeline network into several layers from top to bottom, and each layer contains several independent sub-pipeline networks so that the calculation of each sub-pipeline network can be performed independently. The method reduces the size of the single solution equation set and makes the solution of each sub-pipe network in each layer realized in parallel, thus effectively improving the efficiency of simulation calculation. Finally, this paper analyzes the calculation accuracy and efficiency of the algorithm based on a numerical case of a complex pipe network. The results show that compared with the traditional direct solution method, the layered algorithm can improve the simulation speed under the premise of maintaining the same calculation accuracy. In this case, the average acceleration ratio reaches about 2 times.