This study analyzed site effects including PGA and empirical transfer functions at 15 selected surface–downhole stations by using ground motion recordings of earthquakes with ML > 4 during 2012 and 2013 in Taiwan. In addition, we used all strong motion recordings of four large earthquakes (ML > 6) to generate intensity distribution maps and assess the differences in magnitude at the surface and downhole. The site amplification factors of the PGA were calculated using the ratio between the surface and downhole recordings. The mean PGA amplification factors ranged from 2 to an exaggerated value of 20 at different stations. In addition, the power law relationships between the PGAs at the surface and downhole were evaluated to understand how amplification varies as PGA increases. Strong ground motions with and without site effects throughout Taiwan could be observed by comparing intensity distribution maps generated using the surface and downhole accelerations from four large earthquakes with magnitudes > 6. Empirical transfer functions derived using the single-station and two-station methods at the same stations showed comparable dominant frequencies and amplification factors; however, the empirical transfer function derived using the two-station method showed clearer resonance peaks, not only at fundamental frequencies but also at higher mode resonance frequencies. The HHSR and the HVSR were highly similar, particularly at medium frequencies. This finding indicates that the HVSR can be used instead of the HHSR when only the surface recording is available. Moreover, the local magnitudes calculated using surface recordings were higher than those calculated using downhole recordings. The differences are attributed to the amplification caused by the sedimentary layers and resultant in 0.36, 0.46 and 0.49 on average for events with ML of > 6, 5–6, and 4–5. Furthermore, HHSRs at 5–10 Hz and 1.1–1.7 Hz were strongly correlated with PGA amplifications and ML differences, respectively.