The challenge of stabilizing polymer nanocomposites lies in the fact that nanoparticles tend to phase separate from the polymer melt due to an entropic ‘depletion attraction’ between nanoparticles. Additionally, composites of polymer and nanorods show a decrease in miscibility with increasing nanorod aspect ratio [U. K. Sankar and M. Tripathy, Macromolecules, 2015, 48, 432–442; U. Erigi, U. Dhumal and M. Tripathy, J. Chem. Phys., 2021, 154, 124903]. In this work, we have studied the structure and phase behaviour of polymer–Janus nanorod mixtures using Polymer Reference Interaction Site Model (PRISM) theory and molecular dynamics simulations. The composite system of polymer and Janus nanorods of two different thicknesses, at various Janus nanorod densities, and for different interaction strengths between polymer and attractive sites of Janus nanorods (ε_pa), is investigated for their miscibility and self-assembly. At low Janus nanorod density, PRISM theory predicts transitions from the entropic depletion-driven contact aggregation of Janus nanorods to a well-dispersed phase to the bridging-driven phase separation of Janus nanorods, with increasing ε_pa. This behaviour is similar to earlier predictions for homogeneous nanorods. However, molecular dynamics simulations do not confirm the bridging-driven phase separation at high ε_pa predicted by PRISM theory. We find that both PRISM theory and molecular dynamics simulations are in agreement in the intermediate and high Janus nanorod density regimes. PRISM theory predicts, and simulations confirm, that at high Janus nanorod densities, the system undergoes a transition from depletion-driven macrophase separation to dispersion to chemical anisotropy-driven self-assembly with increasing ε_pa. The self-assembly at high ε_pa is mediated by the polymer. At intermediate Janus nanorod densities, the usual transition from an entropic depletion-driven macrophase separation to dispersion is predicted at low ε_pa. At high ε_pa, both PRISM theory and molecular dynamics simulations show transition to a state that is simultaneously macrophase separated and microphase separated (self-assembled).