The coupling effect of group pit in the excavation process of super large foundation pit group has a great influence on soil deformation and building structure, and its influence degree is more intense when it is constructed in soft strata such as deep silt layer. Therefore, it is of great significance to select the appropriate excavation sequence in the deep foundation pit group project with deep silt soil to reduce the soil disturbance in the protected area. Based on a complex deep foundation pit group project in Shenzhen, the influence of five different construction schemes on the retaining structure and sensitive buildings on both sides of the foundation pit group was explored through finite element three-dimensional numerical simulation. The results show that due to the high rheology and high compressibility of silt and muddy soil, the horizontal displacement of soil has a sudden change compared with the adjacent upper and lower soil layers. It reaches the maximum in the middle and lower part of the side wall in the southwest direction of area C, which is 4.46 mm ~ 7.01 mm, and the horizontal displacement of the diaphragm wall in the southeast direction is 2.67 mm ~ 5.00 mm. When there are multiple foundation pits around the sensitive building, the synchronous excavation of the deep foundation pit and the small foundation pit adjacent to the protected area can further reduce the vertical displacement of the site where the settlement sensitive building is located, which is 31.7 % lower than the original excavation sequence. The lateral displacement of the retaining structure is the smallest when the excavation is completed under the condition of excavating the deep and long foundation pit first and then constructing the small pit. However, the synchronous excavation of the deep and long foundation pit and the adjacent foundation pit can reduce the time effect of the group pit, and further coordinate and control the final deformation of the foundation pit after long-term construction.