Taking a complex practical project that the sea embankment undercrossing an existed expressway bridge in deep soft soil region as research case, utilizing the 3D finite difference numerical simulation as research method, and considering the special reinforcement design, a detail engineering influence analysis for the existed end-bearing pile foundation induced by filling was conducted. The results showed that: 1) Based on the dynamic design optimization by CAD&CAE, the optimized reinforcement scheme, i.e., bored pile + frame connection beam + high pressure jet grouting, was determined, the frame structure showed good integrity and synergistic force characteristics, and the high-pressure jet grouting would effectively improve the engineering properties of soft soil, the “hard crust layer” effectively reduced the consolidation deformation of overlying soft soil; 2) Under the action of additional loading, pressure arch was formed in the frame structure, extrusion induced from transverse direction could be reduced effectively, the additional horizontal displacement of piles under both ramps would be effectively controlled, and in the direction along bridge axis, large area additional loading was transferred to additional bending moment of bored piles and axial force of connecting beams, so the additional bending moment increment of piles could be effectively controlled, after filling, the maximum horizontal displacement on pile top was 4.38 mm, and the maximum increase of compressive stress was less than 0.9 MPa, which met the control requirements well; 3) The whole supporting structure could be regarded as the sleeve around bridge piles, accompanying with symmetrical thin-layer filling of embankment, it would effectively reduce the relative deformation between bridge piles and surrounding soil, and played a significant role in controlling the axial force increment of piles. To sum up, finely numerical simulation effectively overcame the limitations of technical specifications method in complex engineering applications, and provided a necessary technical support in evaluation applicability of project scheme and effect.