This study investigated interdecadal variability of June–October (JJASO) the large and small warm pools in western Pacific and their association with rainfall anomalies using station and reanalysis data between 1958 and 2008. The results indicated that the large and small warm pools in western Pacific showed an interdecadal shift around 1986. The large warm pool years over western Pacific were found after 1986, whereas the small warm pool years were often seen throughout the periods before 1986. The analysis results also showed that there were obvious interdecadal variability in JJASO rainfall in Southeast China and warm pool in western Pacific. Between 1958 and 1985 (small warm pool years), the decrease in rainfall was associated with tropospheric moisture divergence and sinking motion over Southeast China and warm pool in western Pacific. However, between 1986 and 2008 (large warm pool years), the increase in rainfall was associated with tropospheric moisture convergence and ascending motion. Further analysis showed that large warm pool contributed to the increase in surface latent heat fluxes over warm pool in the western Pacific. Thus, there was an increase in the amount of water vapor over Southeast China and warm pool in western Pacific, which contributed to increased rainfall in these regions.