Cloud-top height is a useful parameter with which to elucidate cloud vertical growth, which often indicates severe weather such as torrential rainfall and thunderstorms; it is widely used in meteorological research. However, general cloud-top height estimation methods are hindered by observational and analytical constraints. This study used data from DIWATA-1, the Philippines’ first microsatellite, to overcome these limitations and successfully produce sophisticated three-dimensional cloud models via stereo-photogrammetry. High-temporal snapshot 200-ms-interval imaging of clouds over Iloilo, Philippines, is performed. Two types of telescopes were used to capture 30 stereoscopic cloud images at ~60- and ~3-m ground sampling resolutions; these were used to construct three-dimensional cloud models with 40- and 2-m vertical resolutions, respectively. The imaged clouds have heights of 2.0 to 4.8 km, which is below freezing level for the Philippines and typical of stratocumulus and cumulus clouds. The results are validated using cloud-edge heights determined by measuring the distance from the clouds to their ground shadows. An RMSE of 0.32 km and a maximum difference of 0.03 km are found for the low- and high-resolution telescopes, respectively. For further validation, the results are compared with cloud-top heights estimated from HIMAWARI-8 images captured on the same day, yielding an average vertical difference of 0.15 km and a maximum difference of 1.7 km.