The invention discloses a prefabricated box culvert structure with adjustable height. The prefabricated box culvert structure comprises a prefabricated box culvert body composed of a horizontal top plate and vertical side walls arranged at the two sides of the horizontal top plate, and two wedge-shaped assemblies arranged at the bottoms of the vertical side walls and used for adjusting the vertical height respectively; the cross section of the box culvert body is n-shaped or O-shaped, the bottom of each side wall is longitudinally wedge-shaped, each wedge-shaped assembly comprises a connector,a wedge-shaped block and a wedge block fixing piece, the connectors are fixedly arranged at the bottoms of the vertical side walls, and the wedge-shaped blocks are fixedly connected with the connectors through the wedge block fixing pieces and arranged above the inner side of a segment lining of a shield tunnel. According to the prefabricated box culvert, by adjusting the relative positions of the wedge-shaped assemblies and the box-body vertical side walls in the longitudinal direction, the height of the prefabricated box culvert is adjusted, the distance between the top surface of the prefabricated box culvert body and the road surface/rail surface is accurately adjusted to eliminate or reduce cumulative errors of the construction conduction of the shield tunnel, the inner diameter of the tunnel is reduced, and the investment is saved; the prefabricated box culvert is simple in structure, reasonable in design and good in application effect.