The accurate modeling of spin-orbit coupling (SOC) effects in diverse complex systems remains a significant challenge due to the high computational demands of density functional theory (DFT) and the limited transferability of existing machine-learning frameworks. This study addresses these limitations by introducing Uni-HamGNN, a universal SOC Hamiltonian graph neural network that is applicable across the periodic table. By decomposing the SOC Hamiltonian into spin-independent and SOC correction terms, our approach preserves SU(2) symmetry while significantly reducing parameter requirements. Based on this decomposition, we propose a delta-learning strategy to separately fit the two components, thereby addressing the training difficulties caused by magnitude discrepancies between them and enabling efficient training. The model achieves remarkable accuracy (mean absolute error of 0.0025 meV for the SOC-related component) and demonstrates broad applicability through high-throughput screening of the GNoME dataset for topological insulators, as well as precise predictions for 2D valleytronic materials and transition metal dichalcogenide (TMD) heterostructures. This breakthrough eliminates the need for system-specific retraining and costly SOC-DFT calculations, paving the way for rapid discovery of quantum materials.