Under vacuum negative pressure, the deformation and strength characteristics of soft soil have a close relationship with the loading mode. Firstly, we carry out the vacuum consolidation test to the filled soft soil. Based on the monitoring of foundation settlement and vacuum degree, we compare the foundation settlement law and consolidation effect under different loading modes. Adopting FLAC3D, we establish elastic-plastic 3D numerical simulation model to simulate the soft soil by different loading modes, the result of which is compared with the real-measured data of field test to probe into the mechanism of the effect of the loading mode on consolidation of soft soil. The research indicates that taking multi-stage loading is more advantageous than that of the instantaneous loading to the consolidation of soil when vacuum preloading is adopted to consolidate soft soil foundation. So it is recommended to use the multi-stage loading pattern for the vacuum loading in the project.