Although the synthesis of single atom catalysts (SACs) has attracted intensive attention for the hydrogen evolution reaction (HER), realizing the precise control of the structure of atomic catalysts and the electronic metal–support interaction is still highly challenging. The understanding of SACs at the atomic level is particularly important for further improving their electrochemical performances. Herein, we have reported the synthesis of a spinel Mn3O4 supported Pt SAC (PtSA–Mn3O4) based on the in situ precise anchoring of the Pt atoms in the octahedral sites for the first time. The strong interactions between Pt and Mn3O4 have significantly modulated the electronic structures with an optimized d-band center and binding strength of intermediates. In an alkaline environment, the catalyst shows an excellent HER performance with an ultra-low overpotential of 24 mV at 10 mA cm−2 and a high mass activity of 374 mA mg−1Pt (50 mV), which are superior to those of 20 wt% Pt/C and the most reported high-performance catalysts. This work has supplied insightful information for the rational design of efficient SACs with high controllability and superior performances.