Sea surface dynamic height (SSDH) anomalies estimated from long-time inverted echo sounder (IES) data using gravest empirical mode method are compared with satellite altimeter data. The IES-derived SSDH anomalies agree well with the altimetric SSDH anomalies, although the IES-derived SSDH variation is slightly underestimated. We calculate power spectra of these SSDH anomalies to discuss time-scale dependency of their differences. The differences between two SSDH anomalies are found mainly caused by components with the periods from 50 days to 100 days, which correspond to meso-scale eddies or small meanders of the Kuroshio. These differences result in smaller variation of the IES-derived SSDH.