Advanced integrated circuit (IC) systems increasingly utilize chiplet-based packaging with complex $2.5 \mathrm{D} / 3 \mathrm{D}$ structures and dense Through-Silicon Via (TSV) arrays. While the Finite Element Method (FEM) provides high-fidelity thermal simulation for these systems, its computational efficiency degrades significantly when generating and optimizing meshes for intricate geometries. To address these performance limitations while preserving simulation accuracy, we present NeuralMesh, a novel framework that accelerates thermal analysis of chiplet-based ICs. Our approach integrates deep learning and geometric analysis to optimize mesh generation without the need for iterative refinement steps. NeuralMesh first employs an enhanced segmentation model to predict thermal distributions based on geometric, material, and power parameters. These predictions, combined with key geometric features, guide the optimization of an initial coarse FEM mesh. By eliminating traditional iterative mesh refinement, our framework achieves up to $45.00 \times$ mesh generation speedup while maintaining thermal accuracy within 0.8% of commercial COMSOL simulations. It reduces the number of mesh elements in unimportant areas, which represents a speed improvement of the subsequent thermal simulation. This advancement enables rapid yet precise thermal analysis essential for modern IC package design.

Thermal management in 3D ICs is increasingly challenging due to higher power densities. Traditional PDESolving based methods, while accurate, are too slow for iterative design. Machine learning approaches like FNO provide faster alternatives but suffer from high-frequency information loss and high-fidelity data dependency. We introduce Self-Attention UNet Fourier Neural Operator (SAU-FNO), a novel framework combining self-attention and U-Net with FNO to capture longrange dependencies and model local high-frequency features effectively. Transfer learning is employed to fine-tune low-fidelity data, minimizing the need for extensive high-fidelity datasets and speeding up training. Experiments demonstrate that SAUFNO achieves state-of-the-art thermal prediction accuracy and provides an $842 \times$ speedup over traditional FEM methods, making it an efficient tool for advanced 3D IC thermal simulations.