The nature of the Fokker-Planck equation, proposed by Kirkwood, for the distribution function of polymer chain configuration is investigated in detail. Average coordinates equation and thermodynamic laws are derived from this diffusion equation. Thermodynamic formulation is deduced with the aid of introduction of affinities. The solution of the diffusion equation is given in terms of the eigenfunction of a self-adjoint operator derived from the original diffusion equation according to Kirkwood's theory. The relations among excitation function, relaxation function and response function are shown to be reflections of similar relations among the distribution functions themselves, and the correlation function is calculated. The irreversible entropy production is given in terms of the relaxation time spectrum. The Rouse chain is investigated as an illustration.