In the ultra-deep soft soil area, the vacuum preloading treatment may have adverse effects on the adjacent composite foundation. It is of great significance to analyze these effects and seek practical prevention and control methods. Based on the practical project in ultra-deep soft soil area, a plane strain model was established to restore the vacuum preloading process, explored the impact on composite foundation, and analyzed the effects of countermeasures. Results showed that: (1) the horizontal displacement caused by vacuum preloading was the largest at the site edge, and the deformation of the transition zone between the site edge and the composite foundation was severe, which bearded the main horizontal and settlement deformation difference between the two areas. (2) For the soft soil with low permeability, settlement caused by vacuum preloading was mainly concentrated within 15m below the surface, and the contribution of deep prefabricated vertical drain (PVD) to the settlement was very low. The negative pore pressure experienced the transmission process from the PVD to the soil, from top to bottom. (3)The pore pressure difference between the PVD and the soil decreased with the increase of the depth of the PVD. (4) The lateral displacement of side pile was the largest. The analysis of tension, bending and shear showed that bending moment was the control index of pile failure. The pile group may be damaged from the side pile and then to the foundation center. (5) Increasing the distance between the site to be treated and the subgrade, pretreatment of vacuum preloading before the construction of composite foundation, shortening the length of PVD near subgrade and adding reinforced concrete support on the roadside were all effective measures to control the deformation and stress of composite foundation.