In this study, experimental investigations were carried out on thin-ply and thick-ply countersunk interference fit joints. A comparative study of the mechanical behaviour and hole wall damage during static installation of thin-ply and thick-ply specimens with varied interference sizes were carried out. The effect of interference fit on the strength of countersunk composite bolted joints with different thicknesses of prepreg was investigated in detail under quasi-static tensile loading. The internal damage and failure mechanisms of thin-ply and thick-ply interference joints were investigated by SEM micrographs. The thin-ply specimens had lower installation forces and the initial damage of the thin-ply interference interface was less than that of the thick-ply for the same interference size. The thin-ply can still suppress the generation and propagation of the damage in the load-bearing of the interference connection. More importantly, thin-ply laminates can accommodate more substantial interference sizes than thick-ply laminates and have higher load-bearing strengths of approximately 10–20% more for the same interference size. Thin prepregs can be used to facilitate the design process and improve the structural properties of composites, providing new perspectives for improvements and innovative applications of interference joining technology.