Protein A (SpA) affinity chromatography has been widely used for the purification of immunoglobulin G (IgG). However, the molecular mechanism of the affinity between IgG and SpA remains unclear. In this work, molecular dynamics simulations and molecular mechanics-Poisson-Boltzmann surface area analysis were performed to investigate the molecular mechanism of the affinity interactions. It is found that hydrophobic interaction contributes more than 80% to the binding free energy, while electrostatic interaction plays a minor role (<20%). Through free energy decomposition and pair interaction analysis, the hot spots of the SpA-hIgG1 complex are identified. For hIgG1, the hot spots include the residues of I253, H310, Q311, D315, K317, E430, and N434. For SpA, residues F132, Y133, H137, E143, R146, and K154 contribute significantly. Furthermore, helix I of SpA binds Fc through hydrophobic interaction, while helix II mainly provides electrostatic interaction that determines the binding selectivity to different Igs. Finally, the binding motif of SpA is constructed, which would help design novel high-affinity ligands of IgG.