Response history analyses are usually conducted to evaluate seismic performance of buildings. Since azimuth-dependent buildings are quite common in practice, bidirectional ground motions are considered to be important input motions for the analyses. Based on RotDpp target response spectrum that is widely used to characterize seismic loads of bidirectional ground motions, this study proposes a method to generate spectrum-matched bidirectional time histories using Hilbert–Huang Transform (HHT). To demonstrate applicability of the proposed method, 15 pairs of spectrum-matched bidirectional time histories are generated by the proposed method for a nuclear power plant site. The study further discusses compatibility between these generated bidirectional time histories and the RotDpp target response spectrum. After that, these spectrum-matched time histories are applied to calculate floor response spectra of a service building for a nuclear power plant. After analyzing relative errors of the calculated floor response spectra, advantages of the proposed method are demonstrated. The study finds that, bidirectional time histories generated by the proposed method well match the RotDpp target response spectrum, and they could also provide accurate seismic response analysis of three-dimensional buildings.