An advanced direct half-plane time-domain boundary element method (BEM) was applied to obtain the seismic response of a linear elastic irregular surface including periodically distributed semi-sine shaped valleys subjected to propagating obliquely incident plane SH waves. After developing the method for complex multiple surface topographies, some verification examples were solved and compared with those of the published works. Then, the transient response of a rough surface with 2–16 semi-sine shaped valleys was determined as synthetic seismograms. In this regard, the depth ratio of the valleys was sensitized. Finally, amplification patterns of the surface were presented in some cases. The results showed that the method was able to analyze the multipart models in the time-domain. Moreover, the response of the sinusoidal corrugated surfaces was very effective against seismic waves in forming different patterns. The method was recommended to researchers for transient analysis of complex engineering structures and composite materials in nanoscale.