M-N-C catalysts with nitrogen-coordinated metal single-atom active sites have demonstrated high activity for hydrogen storage materials, but their stability in this application remains uncertain. This study addresses this issue by using nickel phthalocyanine (NiPc) molecules on MgH₂ particles as a model system. It is found that the N-coordinated high-valence Ni single atoms in the NiN₄ active site are unstable in the reducing environment of hydrogen storage, spontaneously evolving into zero-valence Ni, forming a Ni₁-Mg single-atom alloy (SAA). The Ni₁-Mg SAA exhibits remarkable stability in catalyzing Mg hydrogen storage reactions. Furthermore, it demonstrates comprehensive catalytic activity for each step of hydrogen absorption and desorption from Mg, surpassing the efficiency of the NiN₄ active site, especially in the critical steps of hydrogenation and dehydrogenation. Overall, the catalytic performance of Ni₁-Mg SAA is superior to most known nickel-based catalysts. This evolutionary process is also observed in FePc, CoPc, and tetraphenylporphyrin nickel (Ni-TPP), suggesting that this reducing transformation is a universal phenomenon for MN₄-type active sites in hydrogen storage catalysis.