It is possible for nuclear power plant located in near fault zone with the development of nuclear power plant construction. In this paper, 15 sets of far-field earthquakes ground records and 14 sets of near-field earthquake ground records are selected in terms of ATC-63 and the seismic fragility curves of isolated and non-isolated AP1000 nuclear plant shield building in terms of different performance indices are compared based on IDA and MSA methods. The effect of base isolation effect and the degree of aseismic safety margin coefficient improvement are evaluated. The results show that, base isolation of AP1000 nuclear island can play an effective role in reducing the slight damage, medium damage and severe damage probability of nuclear shield building subjected to near-field earthquake. The base isolation would deteriorate the collapse damage as the collapse probability of shield building with base isolation greater than without base isolation but there is still sufficient damage safety margin, so it is feasible to establish it in non bedrock field.