Pipe jacking technology has the advantages of fast construction speed, high economic benefit, and small impact on the urban environment, and mechanical vibration and mechanical soil interaction will lead to the settlement of upper part of pipe jacking and surrounding soil. So, the solution of soil settlement problem is of great significance for underground engineering construction. The soil loss, additional stress, and friction during the construction of rectangular pipe jacking are the main factors that cause the surface settlement. Aiming at the problem of surface settlement caused by pipe jacking in no. 6 subway in Kunming, the formation deformation caused by additional stress and friction force on excavation surface during pipe jacking process was analyzed by Mindlin’s displacement solution, and the formation deformation caused by soil loss was analyzed by random medium theory. Considering the independence of the three influencing factors, the superposition of the three types of stratum deformation was the superposition model of surface settlement, and the model was compared with the empirical method and the measured settlement data to verify its practicability and reliability. The results showed that the surface vertical settlement curve was roughly in the shape of “S,” which can be divided into uplift occurrence area, sensitive settlement area, stable settlement area, and rebound settlement area. Friction force and additional stress caused the uplift of stratum in the front of construction area, and soil loss caused the subsidence of stratum in the rear of construction area. Rectangular pipe jacking in weak stratum caused the soil to move towards the excavation surface, easily causing micro-overexcavation.