Studies on the function-integrated nanocomposites with well-tuned morphologies have received considerable interest. Here, we reported the preparation of mesoporous carbon nanobowl integrated with stoichiometric γ-Fe2O3 and GdPO4 nanoparticles (Fe-Gd/MCN-B) for morphological advantage exploration. Followed by (i) emulsion-induced interface anisotropic assembly of polydopamine, (ii) solvent evaporation-induced sorption of Wells-Dawson-like heterometallic cluster of {Fe6Gd6P6} and (iii) temperature-programmed carbonization, Fe-Gd/MCN-B with the size around 200 nm was isolated. Our in-vitro studies revealed that Fe-Gd/MCN-B showed a 63.0 % amplified photoacoustic (PA) signal intensity as compared with its nanospherical analogue of Fe-Gd/MCN-S owing to the enhanced light harvesting and photothermal conversion on the interface of its nanobowl morphology. Furthermore, the combined magnetic resonance (MR) imagining, drug delivery and photothermal treatment efficacy in Fe-Gd/MCN-B were also validated in-vitro. These results demonstrated that the delicate design of the morphology of function-integrated nanocomposites is an available way for enhanced imaging performance.