In this paper, a new analytical method of symplectic system, Hamiltonian system, is introduced for solving the problem of the Stokes flow in a two-dimensional rectangular domain. In the system, the fundamental problem is reduced to an eigenvalue and eigensolution problem. The solution and boundary conditions can be expanded by eigensolutions using adjoint
relationships of the symplectic ortho-normalization between the eigensolutions. A closed method of the symplectic eigensolution is
presented based on completeness of the symplectic eigensolution
space. The results show that fundamental flows can be described by
zero eigenvalue eigensolutions, and local effects by nonzero eigenvalue eigensolutions. Numerical examples give various flows in a rectangular domain and show effectiveness of the method for solving a variety of problems. Meanwhile, the method can be used in solving other problems.