Based on Hamilton's principle and a cubic Hermite polynomial shape function, first the improved steel-concrete composite box beam element stiffness and mass matrixes with a few numbers of degree were derived by considering many influencing factors such as interface slip, shear lag, shear deformation, and rotational inertia, and then the finite beam element method program was established. The natural vibration frequencies of many steel-concrete composite box beam calculation samples with different spans, degrees of shear connection, and boundary conditions were calculated. The analysis results show that the finite beam element method calculation results are consistent with ANSYS' calculation, thus demonstrating the rationality and validity of the improved steel-concrete composite box beam element stiffness and mass matrixes proposed in this study. Moreover, some meaningful conclusions to engineering design were drawn as follows: The effect of shear lag increases with the order of steel-concrete composite box beam's natural vibration frequency and degree of shear connection. Shear deformation also increases with the order of steel-concrete composite box beam's natural vibration frequency; thus, the shear deformation corresponding to the steel-concrete composite box beam's highorder natural vibration frequency cannot be ignored. The interface slip of steel-concrete composite box beam's high-order natural vibration frequency is negligible; however, the interface slip of steel-concrete composite box beam's low-order natural vibration frequency cannot be ignored.