In the theory of mechanics and/or mathematical physics problems in a prismatic domain, the method of separation of variables usually leads to the Sturm-Liouville-type eigenproblems of self-adjoint operators, and then the eigenfunction expansion method can be used in equation solving. However, a number of important application problems cannot lead to self-adjoint operator for the transverse coordinate. From the minimum potential energy variational principle, by selection of the state and its dual variables, the generalized variational principle is deduced. Then, based on the analogy between the theory of structural mechanics and optimal control, the present article leads the problem to the Hamiltonian system. The finite-dimensional theory for the Hamiltonian system is extended to the corresponding theory of the Hamiltonian operator matrix and adjoint symplectic spaces. The adjoint symplectic orthonormality relation is proved for the whole state eigenfunction vectors, and then the expansion of an arbitrary whole state function vector by the eigenfunction vectors is established. Thus the range of classical method of separation of variables is considerably extended. The eigenproblem derived from a plate bending problem in a strip domain is used for illustration.