To study the deformation characteristics of existing structures induced by rectangular pipe jacking crossing soft soil layers and further clarify the deformation laws caused by pipe jacking construction in soft soil layers, this article is based on a pipe jacking project at an entrance and exit in Nanjing. Firstly, on-site tests of rectangular pipe jacking construction were carried out to analyze the surface and structural deformation laws caused by rectangular pipe jacking crossing bridge foundations and pipelines. On this basis, considering the influence of geological losses on structural deformation, a dynamic numerical analysis model for rectangular top pipe jacking was constructed, and the influences of soil shrinkage rate, box culvert to top pipe spacing, and palm face pressure on the deformation of existing structures were analyzed. The results indicate that as the top pipe section advances step by step, the surface cross-section and pipeline exhibit deformation characteristics of large settlement in the middle and slight uplift on both sides. The deformation characteristics of the bridge foundation mainly manifest as deviation from the direction of the pipe section. Compared to the distance between the box culvert and the top pipe and the pressure on the palm surface, the change in the soil shrinkage rate has the greatest impact on the deformation of existing structures.