Heterojunctions have received much attention because of their perfect charge-separation effectiveness in improving catalytic/photocatalytic activity, but reproducible formation and nonuniform particle size remain ongoing challenges. Numerous metal-oxide clusters with constructions similar to heterojunction nanoparticles, referred to in this study as intramolecular heterojunction compounds, have now been discovered in the literature and may be potential solutions to the aforementioned challenges. The first section of this critical review introduces the concept of intramolecular heterojunction and the constructions, synthetic methods, and tabulation of selected examples. Catalytic reactions using intramolecular heterojunction compounds are systemically surveyed in the second part, including activation of H₂O₂ and O₂ for selective oxidations, electrocatalytic reductions, photocatalytic water splitting, and CO₂ conversion. Finally, future research directions are discussed. In the future, more intramolecular heterojunction compounds may be designed and synthesized following this path, which would undoubtedly benefit research in molecular chemistry and photocatalysis.