Benefitting from the advances made in well-controlled materials synthesis techniques, nanocomposites have drawn considerable attention due to their enthralling physics and functionalities. In this work, we report a new heteroepitaxial mesocrystal-perovskite nanocomposites, (NiFe2O4)0.33:(La0.67Ca0.33MnO3)0.67. Elaborate structural studies revealed that tiny NiFe2O4 nanocrystals aggregate into ordered octahedral mesocrystal arrays with {111} facets together with a concomitant structural phase transition of the La0.67Ca0.33MnO3 matrix upon post-annealing process. Combined magnetic and x-ray absorption spectroscopic measurements show significant enhancement in the magnetic properties at room temperature due to the structural evolution of magnetic NiFe2O4 and the consequent magnetic coupling at the heterointerface mediating via well connected octahedrons of Mn-O6 in La0.67Ca0.33MnO3 and (Ni,Fe)-O6 in NiFe2O4. This work demonstrates an approach to manipulate the exiting physical properties of material systems by integrating desired functionalities of the constituents via synthesis of a self-assembled mesocrystal embedded nanocomposite system.