Two-dimensional heterostructures offer a new route to manipulate phonons at the nanoscale. By performing non-equilibrium molecular dynamics simulations we address the thermal transport properties of structurally asymmetric graphene/hBN nanoribbon heterojunctions deposited on several substrates: graphite, Si(100), SiC(0001), and SiO₂. Our results show a reduction of the interface thermal resistance in coplanar G/hBN heterojunctions upon substrate deposition which is mainly related to the increment on the power spectrum overlap. This effect is more pronounced for deposition on Si(100) and SiO₂ substrates, independently of the planar stacking order of the materials. Moreover, it has been found that the thermal rectification factor increases as a function of the degree of structural asymmetry for hBN-G nanoribbons, reaching values up to ∼24%, while it displays a minimum (∈[0.7,2.4]) for G-hBN nanoribbons. More importantly, these properties can also be tuned by varying the substrate temperature, e.g., thermal rectification of symmetric hBN-G nanoribbon is enhanced from 8.8% to 79% by reducing the temperature of Si(100) substrate. Our investigation yields new insights into the physical mechanisms governing heat transport in G/hBN heterojunctions, and thus opens potential new routes to the design of phononic devices.