In order to suppress the free-surface air-entraining vortex in pump sumps, the three-dimensional unsteady vortex flow in a pump sump was calculated by computational fluid dynamics (CFD) method. The dynamic process of the free-surface air-entraining vortex was simulated. And an experimental model was conducted to verify the CFD method. In this experimental model, a circular plate device was placed between the free surface and the inlet of the bell-mouth to suppress the air entrainment. Furthermore, a parameter called helicity density was adopted to reveal the mechanism of air-entrainment and its suppression. The results showed that the numerical method used in this study can predict the dynamic process of air-entrainment for the free-surface vortex accurately. The helicity density played a very important role in the formation of air entrainment. When the dimple appeared on the free surface, a helicity density tube was formed around the inlet of the bell-mouth. As air entered into water, the other helicity density tube was formed under the free surface. When the two helicity density tubes were connected with each other, the air-core from the free-surface to the inlet of the bell-mouth was formed. This meant that the mechanism of air-entrainment for the free-surface vortex was the connection of the helicity density tubes which provided a passage for air to pass through. Moreover, the circular plate with enough dimension can successfully suppress the air-entrainment through cutting off the helicity density tubes.