This study investigates the influence of sheet thickness and stacking configuration on the formation, quality, and mechanical performance of self-piercing rivet (SPR) joints in AA6061-T6 aluminum sheets. SPR joints were fabricated under controlled, constant process parameters to clarify the effects of upper and lower sheet thickness. Experimental trials were complemented with a validated 2D axisymmetric finite element model to analyze rivet penetration, flaring, and stress–strain evolution. Joint quality indices, including undercut, remaining thickness, and rivet head height, were evaluated alongside microstructural deformation patterns and failure modes. Results demonstrate that thinner upper sheets over thicker lower sheets enhance undercut formation and rivet interlock, while thicker lower sheets reduce strain localization and promote uniform deformation. For configurations with a thick upper sheet, optimized rivet and die geometries were proposed to improve upper sheet piercing and joint quality. Stress analysis revealed that rivet tip and lower sheet regions experience the highest plastic deformation, controlling piercing and mechanical interlock behavior. A regression-based statistical model was developed to predict joint quality indices with high accuracy (MAPE
<
10%) and robustness, enabling systematic optimization of SPR joints. The study provides mechanistic insights into SPR joint formation, highlighting the critical role of sheet thickness configuration, and establishes practical guidelines for designing robust SPR joints for lightweight structural applications.