Based on the energy method considering the second order effects, the natural frequencies of externally prestressed simply supported beam and the compression softening effect of external prestress force were analyzed. It is concluded that the compression softening effect depends on the loss of external tendon eccentricity. As the number of deviators increases from zero to a large number, the compression softening effect of external prestress force decreases from the effect of axial compression to almost zero, which is consistent with the conclusion mathematically rigorously proven. The frequencies calculated by the energy method conform well to the frequencies by FEM which can simulate the frictionless slide between the external tendon and deviator, the accuracy of the energy method is validated. The calculation results show that the compression softening effect of external prestress force is negligible for the beam with 2 or more deviators due to slight loss of external tendon eccentricity. As the eccentricity and area of tendon increase, the first natural frequency of the simply supported beams noticeably increases, however the effect of the external tendon on other frequencies is negligible.