The influence of the complex pre-stress on the circular plate is investigated herein, with which to solve the non-uniform pre-stress distribution problem. According to the strain–stress equation, the motion differential equations of the circular thin plate with complex pre-stress distribution are derived. Based on the Rayleigh–Ritz theory of energy method, the complex pre-stress distribution function and vibration-displacement function are expanded into the cosine trigonometric series, and the approximate analytical solutions of structural free vibration for circular plate are proposed. A circular plate with simply supported boundary condition, for example, the effectiveness of the proposed method is confirmed through numerical calculations and the finite element method verification. The influence of different type’s distribution of welding residual stress on the natural frequency and mode shape for circular plate structure are compared. The proposed approach in present article can be used in arbitrary pre-stress distribution problem.