The propagation of uncertainties in structural dynamic responses, arising from variations in material properties, geometry, and boundary conditions, is of critical concern to researchers in a variety of engineering instances. Conventional methods like high-fidelity Monte Carlo simulation are computationally prohibitive, while existing surrogate models can improve efficiency at the expense of accuracy. To achieve a trade-off between accuracy and efficiency, a Physics-Informed Conditional Variational Autoencoder (PI-CVAE) model is proposed. It integrates a novel dual-branch encoder for time-frequency feature extraction, a learnable frequency-filtering decoder, and a holistic physics-informed loss function so as to enable efficient generation of dynamic responses with high accuracy and adequate physics consistency. Comprehensive numerical analysis of plate structures demonstrates that the proposed approach achieves remarkable accuracy (maximum FRF error < 0.2% and $R^2$ > 0.99) and a computational speedup of 8–11 times in comparison with conventional simulation techniques. By maintaining high accuracy while efficiently propagating uncertainties, the PI-CVAE model provides a practical framework for probabilistic vibration analysis, especially during the acoustic design phase.