The Countersunk composite joints are widely utilized in the load-bearing components of aerospace structures. However, hole-making causes local stress concentration, affecting joints’ bearing capacity. Therefore, a detailed experimental investigation was conducted on the strength under varying parameters including ply thickness, stacking sequence, and interference size in the single-lap countersunk composite joint. The installation force of the thin-ply joint was smaller than that of the thick-ply at the same interference. The initial damage of the thin-ply hole wall caused by the bolt-inserting process was less. The strengths of the two thick-ply joints improved by 10.12% and 9.09% (1.00% interference), respectively, compared with those of thick-ply neat-fit joints. The strengths of the two thin-ply joints increased by 18.18% and 21.78%, respectively, when the interference was increased to 1.44%. SEM imaging revealed that the damage extent of the thin-ply area is smaller with the same interference. Moreover, the fibre kinking angle of the 0° plies at the thick-ply section was more extensive, leading to fibre fracture. Using interference-fit technology to thin-ply laminates could improve the damage resistance of bolted joints and provide a novel idea for applying thin-ply laminates in thin-walled structural components.