Heterojunctions have received a lot of 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 (MOCs) with constructions similar to heterojunction nanoparticles, referred to herein 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, as well as 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 researches in both molecular chemistry and photocatalysis.