This work aims to explore the influence of crystal phase engineering on the photocatalytic hydrogen evolution activity of Ru/C3N4 systems. By precisely tuning the combination of Ru precursors and reducing solvents, we successfully synthesized Ru co-catalysts with distinct crystal phases (hcp and fcc) and integrated them with C3N4. The photocatalytic hydrogen evolution experiments demonstrated that hcp-Ru/C3N4 achieved a significantly higher hydrogen evolution rate (24.23 μmol h−1) compared to fcc-Ru/C3N4 (7.44 μmol h−1), with activity reaching approximately 42% of Pt/C3N4 under the same conditions. Photocurrent and electrochemical impedance spectroscopy analyses revealed that hcp-Ru/C3N4 exhibited superior charge separation and transfer efficiency. Moreover, Gibbs free energy calculations indicated that the hydrogen adsorption energy of hcp-Ru (ΔGH* = −0.14 eV) was closer to optimal compared to fcc-Ru (−0.32 eV), enhancing the hydrogen generation process. These findings highlight that crystal-phase engineering plays a critical role in tuning the electronic structure and catalytic properties of Ru-based systems, offering insights for the design of highly efficient noble metal catalysts for photocatalysis.