This study presents an approach to the free vibration analysis of beams, accounting for lateral shear strain through two independent variables: displacement \(y\) and shear force \(Q\) . The model builds upon the author’s previously developed theory, A New Beam Theory Considering Horizontal Shear Strain, and yields vibration functionals expressed in terms of variables \(y\) and \(Q\) . This study employs the virtual load method, combined with the Lagrange multiplier method, to derive the characteristic polynomial for determining the natural frequencies. Additionally, the parameter optimization method is used to solve the eigenvalue problem under various boundary conditions. The proposed approach accurately captures the influence of lateral shear strain, which significantly affects the structural response of deep beams, short columns, and thick plates. Furthermore, this approach effectively eliminates the shear locking phenomenon, commonly encountered in analyses of structures considering shear strain.