Aerosol effects on deep convective cloud (DCC) have been recognized as one of the complex subjects in climatic studies because of the difficulty in quantifying the sole effect of aerosols on DCC. The complexity further arises if the atmosphere has very strong temporal and spatial variations such as that of Indo-Pacific Warm Pool (IPWP) region. Considering the strong influence of IPWP region on global climate change and water circulation, we investigated aerosol effects on DCC over this region by using data of 2015–2016 El Nino and the 2017–2018 La Nina events. We developed a spectral analysis based framework to identify and decouple the influences of major external factors on aerosol-DCC relationship. We found that temporal variations of aerosols, clouds, and meteorology longer than 2 days’ time scale can have larger influences than their diurnal and spatial variations on acrosol-DCC relationship. By removing the effects of those spatial and temporal variations of different scales, the study suggests that aerosols of IPWP region can affect DCC properties with time lags less than ~5 hours and by increasing cloud-top height, cloud coverage, and DCC number concentration with the increase of aerosols.