The strong ground-motion records selection in structural collapse fragility analysis was studied. To consider the seismic hazard difference within target sites, the conditional mean spectrum (CMS) was used as the target spectrum for ground-motion records selection in the increment dynamic analysis (IDA) method. The CMS was constructed through the China seismic deaggregation and probability seismic hazard analysis. Taking three different 2D structures as examples and based on the seismic safety evaluation of two cities in China, the CMS was constructed to analyze the collapse fragility curves with IDA method, and the results were compared with the results obtained from the uniform hazard spectrum, the code spectrum, and recommended recordings in ATC63. The results indicate that the collapse fragility curve using code spectrum is the steepest, the results of the uniform hazard spectrum and ATC63 are the next, and the suggested method is the flattest. Meanwhile, for the long period 1.5 s structure, the envelope CMS is implemented to consider the influence of the multiple model period effect instead of the single period CMS which underestimates the collapse fragility calculation result significantly for the long period structures.