The China–Russia Natural Gas Pipeline East Line is considered a guarantee for China's natural gas import and supply and an exceptional opportunity to boost natural gas infrastructure in Northeast China, including natural gas storage and connecting pipelines. As a pipeline network covering 14% of China's total land area, it is important to understand the optimal distribution of natural gas storage and carbon emissions to meet China's emission peak and neutrality targets. In this study, we provided an approach using the facility location problem model to determine locations of natural gas storage facilities for prefectural cities in Northeast China within the coverage of the China–Russia Natural Gas Pipeline East Line under five different pipeline layouts, including the current one. Natural gas storage distribution, trunk and branch pipeline length, and total emissions were presented. The results show that the natural gas storage distribution affiliated with the current pipeline route does not have the most optimal distribution and does not have the lowest carbon emission, while the geographical distribution of the cities is more influential for location selection.