An efficient reduced-order modeling (ROM) approach to predict unsteady behavior of partial cavity flows is proposed. The unsteady potential flow along with the cavity effects is analyzed using the boundary element method (BEM). Partial cavity flow is modeled based on the partially non-linear model without re-gridding with some modification. Proposed reduced-order model (PROM) is based on the fluid eigenmodes. The spatial iterative scheme that is usually used to determine the cavity extent is efficiently removed in order to construct the flow eigensystem. Eigenanalysis and reduced-order modeling of unsteady flows over a NACA 16-006 section are performed using the proposed reduced-order modeling approach. Numerical examples are presented to demonstrate the accuracy of the proposed method. Comparison between the obtained results of the proposed method and those of conventional ones indicates that the present algorithm works well with sufficient accuracy. Finally, it is shown that the proposed method is computationally more efficient than the conventional one for unsteady sheet cavitation analysis on hydrofoils.