To calculate the deflection of steel-concrete continuous composite girder accurately, the equilibrium differential equations and the corresponding boundary conditions for calculating the deflection of steel-concrete composite girder were derived by using the energy variational method. The influence of shear deformation of composite girder and the slip effect between steel girder and concrete slab were considered. By introducing the boundary conditions of two-span continuous steel-concrete composite girder under uniformly distributed load, the deflection calculation formula of the steel-concrete continuous composite girder was obtained. The correctness of the deflection calculation formula was also verified. A further analysis of the deflection of steel-concrete continuous composite beams shows that the slip effect reduces the stiffness of steel-concrete continuous composite girder, causes additional deflection, and increases the negative bending moment of the girder at the middle fulcrum, which adversely affects the stress of the concrete slabs. Slip displacement between layers decreases with the increase of shear stiffness of shear connectors. When the shear stiffness of shear connectors is less than 1200 MPa, the additional deflection caused by slip effect is larger, and the influence on the total deflection is greater. The influence of slip effect on the deflection of the composite girder should be considered. However, when the shear stiffness of shear connectors is greater than 1200 MPa, the additional deflection caused by slip effect is small and the influence on the total deflection is small. The influence of slip effect on the deflection of the composite girder can be ignored.