Lacking theoretical analysis, the nitrogen replacement process during emergency maintenance of natural gas pipelines has depended on experience. For optimizing the process, a dynamic fluid model has been established with SPS software and has been used to investigate the replacement time. A series of parameters are examined to investigate the effect of the perforation on the nitrogen replacement strategy. The results indicate that the position of the perforation impacts the replacement time and injecting nitrogen from the farther valve chamber can shorten the time, when it is carried out at only one valve chamber. Further, the optimal decision of nitrogen replacement strategy, injecting nitrogen with only one or two valve chambers, is made by the size as well as the position of the perforation. Then, a semi-empirical phase diagram in terms of the nitrogen replacement strategy is deduced, which provides effective guidance for practical operation of nitrogen replacement.