In an attempt to enhance electrical conductance and improve the formation probability of a molecular junction, a hybrid method was established. Charge transport and conductance-length dependence (exponential decay) in hybrid acene-based molecular junctions was investigated using Density Functional Theorem (DFT) in combination with Non-equilibrium Green’s Function (NEGF) formalism. Lower acenes was employed to explore desired electronic functions in order to diversity the electrical properties and designs of molecular junctions by employing heterogeneous structures. The transmission coefficients T(E), the Frontier Molecular Orbitals (FMO) in consideration of their gap (HOMO-LUMO gap) and the electrical conductance-length dependency were investigated. The results showed that hybrid molecular junctions enhanced electrical conductance and is recommended for anthracene and pentacene molecules. It also showed that the anchoring materials have a significant effect on the HOMO-LUMO gap of the junction. It is also observed that the hybrid molecular junctions showed a non-exponential conductance decay. Lastly, we recommend that the practical implementation of these hybrid molecular junction will bring about a lot discoveries of functionalities and applications in nano electrical circuits.