Defect engineering is an effective approach to improve the gas conversion properties of photocatalysts. However, revealing the defect microstructures and performance enhancing mechanism remain challenges. In this work, the precise content and atomic-level structure of oxygen vacancy in Bi2MoO6/MXene heterojunction photocatalyst was studied by neutron scattering. Pair distribution function analysis shows that the vacancy percentage of oxygen connected with Mo in Bi2MoO6 is 16.6%, and the metal-O bond length decreases near the vacancy. The performance enhancement mechanism of oxygen vacancy in Bi2MoO6/MXene towards photocatalytic NO oxidation was investigated through experiments and density functional theory (DFT) calculations. The optical properties of the heterojunction photocatalyst can be significantly improved by the oxygen vacancies. The exposed Mo atoms at the vacancies greatly benefit the adsorption and activation of reactants, and also accelerate the generation of reactive oxygen species. The NO removal efficiency of the oxygen vacancy-containing Bi2MoO6/MXene heterojunction can reach up to 94.3% under visible light. This work provides a new approach for studying the microstructure and activity enhancement mechanism of oxygen vacancy in photocatalysts.