The governing equation of the bending problem of simply supported thin plate on Pasternak foundation is degraded into two coupled lower order differential equations using the intermediate variable, which are a Helmholtz equation and a Laplace equation. A new solution of two-dimensional Helmholtz operator is proposed as shown in Appendix 1. The R-function and basic solutions of two-dimensional Helmholtz operator and Laplace operator are used to construct the corresponding quasi-Green function. The quasi-Green’s functions satisfy the homogeneous boundary conditions of the problem. The Helmholtz equation and Laplace equation are transformed into integral equations applying corresponding Green’s formula, the fundamental solution of the operator, and the boundary condition. A new boundary normalization equation is constructed to ensure the continuity of the integral kernels. The integral equations are discretized into the nonhomogeneous linear algebraic equations to proceed with numerical computing. Some numerical examples are given to verify the validity of the proposed method in calculating the problem with simple boundary conditions and polygonal boundary conditions. The required results are obtained through MATLAB programming. The convergence of the method is discussed. The comparison with the analytic solution shows a good agreement, and it demonstrates the feasibility and efficiency of the method in this article.