The multiple 3D cracks initiated from the multiple fastener holes frequently occur in aircraft structural components. The fatigue crack growth life prediction of the situation is one of the major concerns and the technically tough work in the multiple-site damage assessment. Our paper investigates the methodology of fatigue crack growth prediction for multiple 3D cracks starting from multiple countersunk fastener holes. An efficient numerical method was proposed in which the computer code was made using the parametrical language of the finite element analysis package. The fast finite element modeling and automatic mesh regeneration, together with a fast cumulative damage technique of fatigue crack growth, were conducted to achieve the life-span numerical simulation for multiple 3D crack growth. The net-section yielding was considered as the criterion to terminate the fatigue life prediction. Two scenarios of a pair of initial asymmetric corner cracks initiated from both sides of a countersunk fastener hole were taken as example problems and analyzed throughout their fatigue crack growth lives. The simulation results agree well with the experimental results.