The PFS method (Partially Floating Sheet pile method) has been frequently used as a countermeasure to reduce settlement during embankment construction due to the edge cutting effect near the embankment toe. However, the anti-seismic effect has not yet been fully discussed. Therefore, to expand the applicability of the PFS method, seismic response analyses for river embankments on sand -clay alternating soft ground was conducted using soil-water coupled finite deformation analysis. As a result, it was shown that the embankment damage (settlement of the embankment crown and horizontal displacement of the embankment toe) caused by the earthquake decreased in the order of no countermeasure, floating sheet pile method, PFS method, and end bearing sheet pile method, which indicates that the anti-seismic effect of the PFS method was confirmed. Moreover, the PFS method was considered to be more effective in suppressing lateral flow, especially near the ground surface, compared with the floating sheet pile method.