This study experimentally and numerically investigates the shear strength and interlayer damage mechanisms of short carbon fiber-reinforced Polyamide 6 (PA6-CF15) composites fabricated via Fused Deposition Modeling (FDM) along the critical ZX build orientation. Using a Taguchi experimental design, the effects of key processing parameters—nozzle temperature, layer thickness, number of outer walls, and post-heat treatment duration—on shear strength were systematically analyzed. Experimental results indicated that PA6-CF15 specimens exhibited higher maximum shear loads compared to neat PA6, although they demonstrated more brittle behavior and lower ductility, primarily due to insufficient fiber bridging in the Z-direction. The optimal parameters for maximizing shear strength were identified as a nozzle temperature of 260 °C, a layer thickness of 0.15 mm, two outer walls, and 80 min of post-heat treatment. Finite Element Analysis (FEA) corroborated experimental findings by revealing stress concentrations near shear notch regions and confirming that optimized parameters enhance interlayer cohesion. Furthermore, comprehensive surface roughness measurements and Scanning Electron Microscopy (SEM) analyses provided detailed insights into damage progression. Higher nozzle temperatures and thinner layers resulted in smoother surfaces and denser structures, which correlated with improved shear strength. SEM images revealed complex failure mechanisms including fiber-matrix debonding, fiber pullout, matrix cracking, and fiber breakage, with evidence of matrix smearing and ductile drawing. The finite element simulations predicted a maximum shear stress of 151.6 MPa and an average shear stress of 23.4 MPa under optimized conditions, aligning well with experimental observations. Among the examined parameters, layer thickness had the most pronounced influence on shear strength, followed by wall line count and heat treatment duration, while nozzle temperature exhibited a comparatively moderate effect. The findings underscore the critical role of process parameter optimization in enhancing the shear strength and overall mechanical performance of FDM-printed short carbon fiber-reinforced PA6 composites, offering valuable guidance for both academic research and industrial applications.