The three dimensional finite element model of composite laminates made of carbon fiber reinforced bismaleimide resin is built, and the natural vibration of the square composite laminates with clamped edges is analyzed. The natural vibration frequencies and modes of laminates without damage are given based on finite element method. The three dimensional finite element models of the same square laminates with non-penetrating damage repaired by two kinds of bonding methods are built. The natural vibration frequencies and modes are also given. It is showed that the three dimensional models can simulate the geometric and physical features of the real composite laminates. It is concluded that the natural vibration frequencies of the composite laminates all increase after it is repaired either by scarf bonding method or scarf and surface bonding method. After scarf bonding repairing, the lowest natural frequency increases about 3.6% and the second natural frequency increases 3.7%. After scarf and surface bonding repairing, the lowest natural frequency increases about 4.5% and the second frequency increases about 6.4%. The natural vibration modes of different repairing models are similar. The increase of natural frequencies may cause temporary vibration of aircraft skin made of composite laminates. The risk of resonance caused by bonding repairing is small.