AbstractOxygen‐inducing controllable surface reconstruction on the transition metal‐based (TMB) materials surface has a great impact on catalytic performance. However, regulating the oxygen coordinative position during the active sites reconstructive process is challenging and poorly understood. Here, the metastable isomeric catalytic site is reasonably designed and fabricated for enhancing photocatalytic hydrogen evolution. Due to the controlled coordinative position of the oxygen atom, a new ternary catalytic site Co‐P(‐‐O) is created, improving the photocatalytic performance of H2 evolution toward 20.7 mmol g−1 in 6 h and 0.56% apparent quantum efficiency. The reconstruction method not only changes the electronic state around the catalytic site but also tunes the adsorption energy of the hydrogen atom. Compared with Co‐Co, Co‐P, Co‐O, and O‐Co‐P catalytic sites, the remarkable Co‐P(‐‐O) sites would drive the H‐atom connecting with the Co‐P bridge style achieving the best performance and excellent stability. Such a reconstructed catalytic site is also proved efficient in electrocatalysis and photo‐electrocatalysis systems. In conclusion, this work provides a new insight that the controllable isomeric catalytic site reconstruction strategy can dramatically enhance the catalytic performance.