Realizing highly efficient photocatalytic hydrogen evolution reaction (HER) is a key challenge. Herein, a (FFV)2PdCl2 complex is developed with dynamic coordination engineering between the PdII site and Fluoflavin (FFV) ligands, and couple it with graphite carbon nitride (g‐C3N4) ultrathin nanosheets to construct a novel Z‐scheme heterojunction ((FFV)2PdCl2/C3N4). The resultant heterojunction delivers a HER activity of 648 µmol h−1 under visible light (λ ≥ 400 nm) illumination and an apparent quantum yield up to 40.1% at 400 nm, far superior to those g‐C3N4‐based catalysts reported previously. Mechanistic and theoretical studies reveal that the dynamic coordination between the PdII site and FFV ligands not only significantly accelerates the electron transfer from g‐C3N4 to (FFV)2PdCl2 and then to the PdII sites via a Z‐scheme mechanism, but also effectively maintain the efficacy and stability of the PdII active sties, and thus the (FFV)2PdCl2/C3N4 with a ultralow Pd‐loading amount (ca. 0.1 wt.%) exhibits the impressive activity and durability. The present dynamic coordination and structural evolution of (FFV)2PdCl2 are also applicable for significantly improving the HER performance of other semiconductors, thus paving a potential way for manufacturing highly efficient and active H2 production systems.