<p>A fundamental prerequisite for a reliable design of composite structures containing multi-scale reinforcements is the establishment of clear structure–property relationships. In this study, a unified numerical framework consisted of structural scale analysis and micro-scale material modeling is developed to investigate free vibrations of silica nanoparticle/short glass microfiber/polymer hybrid nanocomposite plates, considering three geometric configurations: rectangular, triangular and elliptical plates resting on an elastic foundation under various boundary conditions. A multi-phase micromechanical method capturing critical microstructures is proposed to predict mechanical properties of ternary nanocomposites. The first-order shear deformation theory is adopted to model the nanocomposite plate. The total potential energy of the system is formulated and minimized using the p-Ritz method to obtain natural frequencies. The effects of key parameters, including content and size of nano-silica, thickness and modulus of interphase formed between the nanoparticle and polymer matrix, aspect ratio and percentage of microfiber, elastic foundation stiffness, and plate geometric characteristics (e.g., length-to-width or diameter ratios) are thoroughly investigated. The incorporation of silica nanoparticles into a short glass fiber-reinforced polymer matrix improves the natural frequency of the resulting nanocomposite plate, and reducing nanoparticle diameter further increases it. Moreover, a thicker and stiffer interphase layer can raise the fundamental natural frequency in all geometries studied. The clamped boundary conditions lead to higher frequencies due to increased structural constraint. The presented numerical methodology establishes a framework to design the hybrid nanocomposite structures with superior mechanical performance.</p>