Lightweight design of structures has been widely used in the transportation, aerospace and electronics industries because of its advantages in reducing energy consumption, reducing emission and improving environmental performance. This study investigates the effects of welding parameters on microstructural evolution and joint performance in friction stir welding lap joints using 6061-T6 aluminum alloy and carbon fiber-reinforced polymer (CFRP). The microstructure of weld surface and the cross section of the joint is systematically examined to analyze surface defects, material softening characteristics, plastic deformation distribution and micropore filling. Experimental results demonstrate that the increased heat input enhances the plastic flow of the material and deepens the shoulder influence zone to 0.54 mm. The optimized welding parameters can inhibit the formation of micropores caused by insufficient material flow, and the defect rate of joints is 8.03%, which increases the resistance to crack propagation and enhances the shear strength of joints. The optimized joints achieve a maximum lap shear strength of 32.9 MPa, representing 63.1% of the CFRP base material strength.