Abstract: Horizontal and vertical ground motions should be considered for both seismic design and evaluation of critical infrastructures such as nuclear power plant structures. Seismic capacity of the nuclear containment under horizontal ground motions has widely been studied. However, the effect of vertical ground motions on seismic fragility analysis of the nuclear containment has been little studied. Meanwhile, there are usually two methodologies for selecting horizontal and vertical ground motions: 1) horizontal ground motions and associated vertical ground motions are selected via the methodology making horizontal ground motions match horizontal target spectra; 2) vertical ground motions and associated horizontal ground motions are selected via the methodology making vertical ground motions match vertical target spectra. However, two above-mentioned selection methodology could not make horizontal and vertical ground motions simultaneously match horizontal and vertical site-specific target spectra. This paper proposed a selection method making ground motions simultaneously match horizontal and vertical ground motions and investigated the effect of vertical ground motion on seismic fragility analysis of a CPR1000 nuclear containment: The limitation of selection methodology of horizontal and vertical ground motion based on horizontal target spectrum was analyzed; An efficient algorithm was proposed for selection of ground motions by making horizontal and vertical ground motions simultaneously match associated horizontal and vertical site-specific spectra; Horizontal and vertical ground motions were selected for a specific site located in China via the proposed method of this paper; Fragility analysis under only horizontal ground motions and under both horizontal and vertical ground motions were respectively analyzed via incremental dynamic analysis; Fragility analysis with confidence under only horizontal ground motions and under both horizontal and vertical ground motions were respectively performed via safety factor method; Finally, fragility curves and high confidence of low probability of failure values were obtained. The results demonstrate that selected vertical ground motions only based on horizontal target spectra might overestimate vertical target spectra values of real vertical ground motions, and selected horizontal and vertical ground motions via the methodology proposed by this paper could well match horizontal and vertical site-specific target spectra; Vertical ground motions have a large effect on seismic capacity and fragility analysis results of a nuclear containment. It is suggested that the selection methodology of ground motions should make horizontal and vertical ground motions simultaneously match horizontal and vertical site-specific target spectra and vertical ground motion should be considered for seismic capacity and seismic fragility analysis of the containment in the future.