This paper is concerned with the dynamic analysis of simply-supported steel-concrete composite beams under moving loads. Considering the interface slip between steel girder and concrete slab, the governing motion equations are derived from the direct balanced method. By variable separation approach, the analytical solution of natural frequencies and mode shapes are obtained, as well as the orthogonal conditions. Then the dynamic responses of the composite beam under moving loads are analyzed, and compared with the experimental results. The analysis results show that the governing motion equations become more complicated when interface slip is taken into account, and the dynamic behaviors are significantly influenced by the shear connection stiffness. In the dynamic calculation of composite beams, the global stiffness should not be reduced as the same factor to all orders, but as different ones according to the dynamic stiffness reduction factor (DSRF), to which should be paid more attention in calculation, design and experiment, or else great deviation is inevitable.