Thin-ply CFRP laminates with ply thickness less than 0.05 mm exhibit superior strength than conventional CFRP laminates. To elucidate the damage behavior of CFRP laminates with different layer thicknesses, we performed progressive damage analyses in open-hole compression (OHC) and filled-hole compression (FHC) tests. Finite element analyses incorporating continuum damage mechanics with 3D-Hashin criterion and cohesive zone model were used to simulate the progressive damage failure. The failure mode and morphology estimated by the numerical simulations are consistent with the experimental results. Furthermore, the orders of open-hole and filled-hole (without fastening torque and with 7.0 Nm fastening torque) compressive strengths obtained from the experiments are in good agreement with the simulation results. The results of progressive damage analyses confirm that thinner plies exhibit higher open-hole and filled-hole compressive strengths than thicker ones.