This paper pioneers a novel approach in electromagnetic (EM) system analysis by synergistically combining Bayesian Neural Networks (BNNs) informed by Latin Hypercube Sampling (LHS) with advanced thermal–mechanical surrogate modeling within COMSOL simulations for high-frequency low-pass filter modeling. Our methodology transcends traditional EM characterization by integrating physical dimension variability, thermal effects, mechanical deformation, and real-world operational conditions, thereby achieving a significant leap in predictive modeling fidelity. Through rigorous evaluation using Mean Squared Error (MSE), Maximum Learning Error (MLE), and Maximum Test Error (MTE) metrics, as well as comprehensive validation on unseen data, the model’s robustness and generalization capability is demonstrated. This research challenges conventional methods, offering a nuanced understanding of multiphysical phenomena to enhance reliability and resilience in electronic component design and optimization. The integration of thermal variables alongside dimensional parameters marks a novel paradigm in filter performance analysis, significantly improving simulation accuracy. Our findings not only contribute to the body of knowledge in EM diagnostics and complex-environment analysis but also pave the way for future investigations into the fusion of machine learning with computational physics, promising transformative impacts across various applications, from telecommunications to medical devices.