As an important bearing component of the aircraft, the multilayer metal fastener structure is subjected to continuous groundairground cyclic loading. The fatigue cracks occur around the hole of fastener, such as rivets and highlock bolts due to the stress concentration. The traditional nondestructive testing method, however, is difficult to detect those cracks under insitu conditions. The remote field eddy current testing technology breaks the skin effect limitation in principle, and has great advantages in detecting deep hidden defects. Therefore, this paper proposes a new design of remote field eddy current sensor with different structure from the traditional method. The excitation coil is placed coaxially with the detection coil, which is located inside the excitation coil with a magnetic field shunt between them. This kind of structure can greatly reduce the sensor size. The optimal design of the new sensor is obtained by utilizing the finite element simulation. This method analyzes the size of the excitation coil, structure material and composition of the magnetic field shunt. Experimental results show that the new sensor can detect perforation of the fasteners by the 2×02×4 mm (length×width×depth) at a depth of 4mm. With the increasing of the defect length, the signal amplitude is increased greatly.