Abstract TOPEX/POSEIDON (T/P) altimeter measurements from December 1992 to April 1998 were processed to study the sea surface height (SSH) variation in the South China Sea (SCS). Patterns of variance of the SSH deviations from the four-year (1993–1996) mean show that there are three high-variation areas in the deep basin. The first is at the northern basin west of Luzon Island (16°–18° N, 117°–119° E), the second is at the center of the SCS (14°–16° N, 113.5°–114.5° E), and the third is off the central Vietnam coast (12°–13° N, 110°–112° E). From empirical orthogonal function (EOF) analysis, we found that the variations of these three active areas are dominated by annual cycles, but out of phase. The first two areas have the highest SSH in June and the lowest SSH in December. The third one off the Vietnam coast has the highest SSH in February and the lowest SSH in August. The EOF analysis also reveals that the variation of SSH in the SCS has a response to El Niño events.