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<p>This study examines the climatology of cloud phase over Southeast Asia (SEA) based on A-Train satellite observations. Using the combined CloudSat–CALIPSO (CC) data, five main cloud groups are investigated: ice-only, ice-above-liquid, liquid-only, ice-above-mixed, and mixed-only clouds that have annual mean frequencies of 28.6&thinsp;%, 20.1&thinsp;%, 16.0&thinsp;%, 9.3&thinsp;%, and 6.7&thinsp;%, respectively. Liquid-only clouds tend to occur in relatively cold, dry, and stable lower troposphere. The other four cloud groups appear more frequently in relatively warm, humid, and unstable conditions, and their seasonal distributions move with the Asian monsoon and the Intertropical Convergence Zone (ITCZ). Liquid clouds are found to be highly inhomogeneous based on the heterogeneity index (<span class="inline-formula"><i>H</i>_<i>σ</i></span>) from Aqua Moderate Resolution Imaging Spectroradiometer (MODIS), while ice-only and mixed-only clouds are often very smooth. Ice-above-liquid clouds are more heterogeneous than ice-only clouds owing to ice clouds being optically thin. We demonstrate that the distribution of clear-sky <span class="inline-formula"><i>H</i>_<i>σ</i></span> has a long tail towards heterogeneous values that are caused by undetected subpixel cloud within both CC and MODIS datasets. The reflectance at 0.645&thinsp;<span class="inline-formula">µ</span>m (<span class="inline-formula"><i>R</i>_0.645</span>) and brightness temperature at 11&thinsp;<span class="inline-formula">µ</span>m (BT<span class="inline-formula">₁₁</span>) of CC ice-only, liquid-only, and ice-above-liquid clouds show peak frequencies near that of clear sky (<span class="inline-formula"><i>R</i>_0.645∼0.02</span>; BT<span class="inline-formula">₁₁∼294</span>&thinsp;K), which explains why up to 30&thinsp;% of these CC cloud groups are classified as clear by MODIS. In contrast, mixed-only clouds are thick (average top <span class="inline-formula">∼13</span>&thinsp;km), bright (average <span class="inline-formula"><i>R</i>_0.645∼0.6</span>), and cold (average BT<span class="inline-formula">₁₁</span> <span class="inline-formula">∼234</span>&thinsp;K). Cloud phase comparison between CC and MODIS reveals only modest agreement, with the best agreement (73&thinsp;%) occurring between CC ice-above-mixed and MODIS ice clouds. The intraseasonal and interannual behaviors of the all-sky <span class="inline-formula"><i>H</i>_<i>σ</i></span> and spectral signatures follow that of cloud phase and vary with the Madden–Julian oscillation (MJO) and the El Niño–Southern Oscillation (ENSO) phases.</p>