The Empirical Orthogonal Function (EOF) is used to analyze the sea level anomalies in the outflow region of the Indonesian Throughflow, and the results show that multi-scale variations of sea level anomalies exist in the study region. Significant ascending trend in the sea level anomalies with a value of 0.6 cm/a is found from 1993 to 2013. The sea level anomaly in the region shows interannual variation and is correlated with the Niño3.4 index,with a correlation coefficient of up to 0.65, implying positive/negative sea level anomalies during El Niño/La Niña events, respectively. The annual cycle of the sea level anomaly is mainly influenced by the Indonesian Throughflow, the South Java Current and the Eastern Gyral Current, and the semi-annual cycle is mainly caused by the eddy generated by the interaction between the South Java Current and the South Equatorial Current. Analysis also reveals that the sea level anomaly exhibits distinct intraseasonal variation in the outflow region of the Indonesian Throughflow.