We investigated the effects of the propagation path and site amplification of shallow tremors along the Nankai Trough. Using far‐field S‐wave propagation from intraslab earthquake data, the amplification factors at the DONET stations were 5–40 times against an inland outcrop rock site. Thick (∼5 km) sedimentary layers with VS of 0.6–2 km/s beneath DONET stations have been confirmed by seismological studies. To investigate the effects of thick sedimentary layers, we synthesized seismograms of shallow tremors and intraslab earthquakes at seafloor stations. The ratios of the maximum amplitudes from the synthetic intraslab seismograms between models with and without thick sedimentary layers were 1–2. This means that thin lower‐velocity (<0.6 km/s) sediments just below the stations primarily control the estimated large amplifications. Conversely, at near‐source (≤20 km) distances, 1‐order amplifications of seismic energies for a shallow tremor source can occur due to thick sedimentary layers. Multiple S‐wave reflections between the seafloor and plate interface are contaminated in tremor envelopes; consequently, seismic energy and duration are overestimated. If a shallow tremor occurs within underthrust sediments, the overestimation becomes stronger because of the invalid rigidity assumptions around the source region. After 1‐order corrections of seismic energies of shallow tremors along the Nankai Trough, the scaled energies of seismic slow earthquakes were 10−10–10−9 irrespective of the region and source depth. Hence, the physical mechanisms governing seismic slow earthquakes can be the same, irrespective of the region and source depth. Plain Language Summary: The deployment of campaigns and permanent ocean bottom seismometers (OBSs) has enabled us to investigate the activity and physical properties of offshore seismic phenomena. Our knowledge of offshore subsurface structures is still limited; consequently, many studies have used conventional analysis methods with the simplest assumptions. Using observed and synthetic seismograms near the Nankai Trough, we found a limitation in the conventional analysis method applied to OBS data. Thick sedimentary layers, which have been confirmed by seismological studies along the Nankai Trough just below the OBSs, cause an approximately 1‐order overestimation of source parameters for seismic phenomena occurring around the shallow plate boundary. This overestimation may have occurred during the seismic energy estimation of shallow slow earthquakes in Hikurangi, Costa Rica, and Mexico. After correcting for the effects of thick sedimentary layers, we found that the scaled energies of seismic slow earthquakes were 10−10–10−9 irrespective of the region and source depth. This suggests that the physical mechanisms governing seismic slow earthquakes can be the same, regardless of region and source depth. Key Points: Effects of path and site on the seismic energy estimation of slow earthquakes at shallow plate boundaries were investigatedThe assumption of far‐field body waves without thick sediments causes an overestimation of seismic energies for shallow tremorsScaled energies of seismic slow earthquakes at both shallow and large depths range from 10−10 to 10−9 [ABSTRACT FROM AUTHOR]