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Sea level variation is inhomogeneous in different locations, even in the same sea area. In this work, altimetry data is used to analyze the spatial characteristics of sea level change in the South China Sea.Overall, the average sea level variation is correlated with El Nino-Southern Oscillation (ENSO) with a coefficient of 0.65 and a time lag of 3 months; however, the coefficient value and the time lag vary in different areas. According to the spatial pattern of the maximum correlation and corresponding time lag, we divided the South China Sea into four parts: western shallow ocean (WSO), northwestern deep ocean (NDO),southwestern deep ocean (SDO), and eastern deep ocean (EDO). Their correlations with ENSO are calculated separately and compared with each other. It is found that the WSO has the modest interannual fluctuation and rising rate, implying that the coast areas are less influenced, comparing with the islands in the deep oceans.NDO has the strongest interannual variation and rising rate, which means the Xisha and Zhongsha islands here is the most susceptible to the ocean dynamics. Our work sheds light on the spatial variability in the changing patterns of sea level in the South China Sea.