The present invention discloses an optimization method for natural gas pipeline operation under the carbon neutrality target. From the perspective of energy structure adjustment, the present invention proposes a complete low-carbon and low-consumption optimization model of long-distance natural gas transmission network, which is used for fine calculation of multi-energy carbon emissions and energy consumption in the transportation process of natural gas pipeline network; according to different energy structure backgrounds, the corresponding objective function for minimum carbon emissions is established, the optimization algorithm is adopted to solve the objective function for minimum carbon emissions and work out the optimal scheduling scheme. The present invention can realize energy conservation and emission reduction in the process of pipeline transportation and provide technical support for achieving the target of “peak carbon dioxide emissions and carbon neutrality” in the entire natural gas industry of China as early as possible.