The small angular deflection of the spool under the action of non-equilibrium force is a main reason for valve seal failure. In the present study, a prediction model of the valve seal leakage was established considering the sectional shape and channel height of the leakage channel. The effect of spool deflection on the leakage rate was analyzed quantitatively from the results of three-dimensional finite element mechanical analysis. The microscale leakage channel of a contact deformation surface was then generated through the reconstruction of the rough surface with nanoscale precision, deterministic rough-peak contact analysis, and lattice leakage theory. The results showed that the spool deflection was the key factor affecting the leakage rate. The leakage rate was measured on a self-built experimental platform, and the experimental results verified the accuracy of the theoretical calculations.