The appropriate excavation sequence can improve the overall stability of a foundation pit. In this study, eight schemes were created using FLAC3D to examine the impact of the excavation sequence on a foundation pit by analyzing a deep foundation pit in Nanjing, which had an irregular large rectangle shape. The results show that different excavation sequence schemes and different phases of the foundation pit can change the displacement values and the horizontal displacement type. The min–max normalization method was used to score the schemes in terms of six parameters and confirm the best excavation sequence scheme. In addition, the irregular shape of the foundation pit also leads to local differences in the stability of a foundation pit; the wide end is only slightly longer than the narrow end, but its displacement is significantly higher than that of the narrow end, so attention should be paid to reinforcing the weak parts when carrying out the support. This study can inform the selection of the excavation sequence for actual construction processes.