Clay shale is frequently encountered in drilling. With strong hydration capacity, when clay shale contacts with drilling fluid, rock structural and mechanical property will be affected, causing wellbore instability. Acoustic frequency spectrum is a significant parameter in geophysical logging. The influence of hydration on clay shale can be reflected in acoustic logging. Therefore, in order to identify hydration damage and have precise evaluation for hydration damage, a novel hydration damage index has been built on the basis of acoustic frequency spectrum. Meanwhile, considering the influence of hydration, hydrated constitutive model has been proposed using this new index. Results demonstrate that acoustic frequency spectrum has clear modification due to hydration damage. In the hydration evolutionary process, fracture initiation and propagation happen, decreasing acoustic amplitude and dominant frequency. The whole hydration evolutionary process exhibits S curve with clear three stages. In the initial stage, changing ranges of acoustic amplitude and frequency are small. In the middle stage, clear fracture propagation can be noticed and fracture network is formed, boosting the change of acoustic frequency spectrum. Finally, acoustic frequency spectrum becomes stable, meaning hydration damage has reached its limitation. Hydration damage degree is variable with different conditions, but the tendency still remains typical S curve. Stress‐strain curves simulated from hydrated constitutive model are in good agreement with results of uniaxial compressive test, indicating this model can be used to express shale mechanical property in hydration evolutionary process. Findings of this paper can offer theoretical reference for evaluating hydration damage and are advantageous for drilling operation in clay shale formation.