The excavation of the deep foundation pit of subway station may cause excessive deformation of foundation pit and retaining structure and then pose a threat to the safety of surrounding buildings and people. Therefore, it is necessary to analyze the characteristics of ground settlement and lateral displacement of the retaining system of foundation pit caused by deep foundation pit excavation in the Guangzhou composite stratum. Based on 28 subway station projects in Guangzhou, this paper analyses the monitoring data in the process of deep foundation pit excavation and reveals the deformation characteristics of subway deep foundation pit in the Guangzhou composite stratum. The research results can provide data support for the excavation scheme design and environmental control of similar deep foundation pit projects. The results show that: (1) The final deformation of the foundation pit at Guangzhou Metro Station is predominantly within the range of 5 to −15 mm. Monitoring points with settlement values exceeding 30 mm constitute the smallest proportion, while only a limited number of measuring points exhibit surface uplift. The observed ground uplift can be attributed to two primary causes: basement heave and the infiltration of grouting slurry outside the pit. (2) The maximum ground settlement of foundation pit increases with the increase of excavation depth. When the aspect ratio of foundation pit is greater than 15, the maximum ground settlement has an obvious positive linear relationship with it. The insertion ratio of foundation pit retaining structure in the Guangzhou area is mainly concentrated in 0.30–0.59, with an average value of 0.42, and the maximum ground settlement gradually decreases with the increase of insertion ratio. (3) The maximum lateral displacement of the retaining structure of the foundation pit accounts for the largest proportion in the range of −20–25 mm. The maximum lateral displacement of the retaining structure increases with the increase of the excavation depth and the length–width ratio of the foundation pit. The maximum lateral displacement of the retaining structure decreases with the increase of the insertion ratio. There is an obvious “skirting” phenomenon in the granite residual soil foundation pit. Attention should be paid to and the insertion ratio should be appropriately increased in the project. (4) The maximum ground settlement caused by deep foundation pit excavation of a subway station in the Guangzhou area is 0.99–1.90 times of the lateral displacement of foundation pit retaining structure.