Two long-period seismic waves with abundant long-period information were selected from earthquake records databases from all over the world. The frequency and spectrum characteristics of these two seismic waves were investigated with the orthogonal HHT (Hilbert-Huang transform) method, and compared with those of two commonly used seismic waves. A complex high-rise building was selected as a case study, in which a finite element model was established with the ANSYS software, and nonlinear dynamic response analysis was conducted on the complex high-rise building with the four seismic waves mentioned above as an input. The results show that the complex high-rise building has different effects in filtering seismic waves, and it can filter long-period seismic waves significantly. In addition, the structure's seismic response to long-period seismic waves is greater than it is to common seismic waves, and the displacement response is more significant than the acceleration responses.