A computational model is established to investigate the effects of a periodic gust flow on the wake structure of ventilated supercavities. The effectiveness of the computational model is validated by comparing with available experimental data. Benefited from this numerical model, the vertical velocity characteristics in the entire flow field can be easily monitored and analyzed under the action of a gust generator; further, the unsteady evolution of the flow parameters of the closed region of the supercavity can be captured in any location. To avoid the adverse effects of mounting struts in the experiments and to obtain more realistic results, the wake structure of a ventilated supercavity without mounting struts is investigated. Unsteady changes in the wake morphology and vorticity distribution pattern of the ventilated supercavity are determined. The results demonstrate that the periodic swing of the gust generator can generate a gust flow and, therefore, generate a periodic variation of the ventilated cavitation number σ. At the peak σ, a re-entrant jet closure appears in the wake of the ventilated supercavity. At the valley σ, a twin-vortex closure appears in the wake of the ventilated supercavity. For the forward facing model, the twin vortex appears as a pair of centrally rolled-up vortices, due to the closure of vortex is affected by the structure. For the backward facing model, however, the twin vortex appears alternately as a pair of centrally rolled-up vortices and a pair of centrally rolled-down vortices, against the periodic gust flow.