Reducing the phonon thermal conductivity of electrically conducting polymers can facilitate their use as potential thermoelectric materials. Thus, the influence of the coupling between the longitudinal and transverse phonon modes on overall thermal conductivity is explored for binary mixtures of polyaniline (PANI) and polyacetylene (PA) chains by considering various geometricpolymer mixture configurations. The molecular simulations reveal that an increase in the interfacial area available for transverse interactions between dissimilar chains enhances atomic interactions that are orthogonal to the heat transfer direction. As transverse collisions between PA and PANI chains are enhanced, the motion of longitudinal phonons is disrupted, impeding thermal transport. This enhances phonon scattering and reduces longitudinal thermal transport. While there is a nonlinear decrease in the phonon thermal conductivity with increasing interfacial contact area, there is a corresponding linear growth in the nonbonded interaction energies between the different polymers.