We extend the quasi-particle renormalized perturbation theory developed in our previous work [Y.-W. Chang and B.-Y. Jin, J. Chem. Phys. 141, 064111 (2014)] based on nonequilibrium Green's function techniques to study the effects of electron correlation on the charge transport process in molecular junctions. In this formalism, the single-impurity Anderson's model is used as the zeroth-order Hamiltonian of each channel orbital, and the inter-channel interactions are treated by perturbation corrections. Within this scheme, the on-channel Coulomb repulsion and the single-particle spectral line-broadening can be incorporated in the zeroth-order approximation, and thus the Coulomb blockade and coherent tunneling through individual channels can be described properly. Beyond the zeroth-order description, electron correlation can be included through the self-energy corrections in the forms of the second-Born approximation and the GW approximation. The effects of electron correlation on molecular junctions are manifested as the orbital energy correction, correlated transport process, and collisional line-broadening. As an application, we have applied the present formalism to phenyl-based molecular junctions described by the Pariser-Parr-Pople Hamiltonian. The signatures of electron correlation in the simulated current-voltage curves are identified and discussed.