The increasing power densities and intricate heat dissipation paths in advanced 2.5D/3D chiplet systems necessitate thermal modeling frameworks that deliver detailed thermal maps with high computational efficiency. Traditional compact thermal models (CTMs) often struggle to scale with the complexity and heterogeneity of modern architectures. This work introduces 3D-ICE 4.0, designed for heterogeneous chip-based systems. Key innovations include: (i) preservation of material heterogeneity and anisotropy directly from industrial layouts, integrated with OpenMP and SuperLU MT-based parallel solvers for scalable performance, (ii) adaptive vertical layer partitioning to accurately model vertical heat conduction, and (iii) temperature-aware nonuniform grid generation. The results with different benchmarks demonstrate that 3D-ICE 4.0 achieves speedups ranging from 3.61×-6.46× over state-of-the-art tools, while reducing grid complexity by more than 23.3% without compromising accuracy. Compared to the commercial software COMSOL, 3D-ICE 4.0 effectively captures both lateral and vertical heat flows, validating its precision and robustness. These advances demonstrate that 3D-ICE 4.0 is an efficient solution for thermal modeling in emerging heterogeneous 2.5D/3D integrated systems.