Nonlinear properties of materials will be automatically ignored while structural dynamic analysis in ANSYS. And the energy method principle is used to analyze. So it can not be used to calculate the frequencies and modals of prestressed concrete structures directly. Accordingly, prestressing force applied to beam with initial strain method in ANSYS calculate in this paper. The perstressing force influence of the beam is changed to the impact of element materials elastic modulus. Analyze the frequencies and modals of prestressed concrete beams with ANSYS computational procedure by modified ANSYS model. The calculated natural frequencies at all levels prestessing force fit close with the experimental results. It shows that modified ANSYS finite element analysis model is feasible.