Carbon-supported atomic clusters (CACs) have been demonstrated to have significant potential for heterogeneous catalysis; however, their synthesis remains a “black box” process due to the complexities associated with metal migration, aggregation, and carbon structural reconstruction behaviors. Herein, the general formation mechanism of metal clusters is uncovered in defective graphene oxide (DGO) during pyrolysis. First, multiple coordination modes of platinum (Pt) atoms on DGO provide opportunities for their temperature-dependent release, where the highly thermally stable sites (Pt─C2 on edge defect) serve as migration termini and nucleation centers. Notably, the size (from 1.5 to 0.99 nm) of PtCACs can be precisely manipulated by increasing the defect densities of DGO. Moreover, the dynamic evolution process is monitored using multiple in situ technologies, revealing a more intense structural reconstitution of DGO compared to that of graphene oxide, which, in turn, limits the aggregation of metal clusters. Electrocatalytic results revealed a negative relationship between the size of PtCACs and their hydrogen evolution performance, where the PtCACs (size: 0.99 nm) exhibit a high mass activity in HER that is 32 times higher than that of the commercial 20% Pt/C catalyst. This work provides a paradigm for establishing the underlying architecture of CAC synthesis methodology.