We study many-body correlations in the ground state of a general quantum system of bosons or fermions by including an additional Jastrow function in our recently proposed variational coupled-cluster method. Our approach combines the advantages of state-dependent correlations in the coupled-cluster theory and of the strong, short-ranged correlations of the Jastrow function. We apply a generalized linked-cluster expansion for the Jastrow wave function and provide a detailed analysis for practical evaluation of the Hamiltonian expectation value as an energy functional of the Jastrow function and the bare density-distribution functions introduced and calculated in our earlier publications; a simple, first-order energy functional is derived and detailed formulas for the higher-order contributions are provided. Our energy functional does not suffer the divergence as most coupled-cluster calculations often do when applying to Hamiltonians with hardcore potentials. We also discuss possible applications of our technique, including applications to strongly correlated fermion systems.