In large-scale industrial explosions and nuclear detonations, a characteristic cloud structure known as a mushroom cloud is sometimes formed. Mushroom clouds often contain hazardous chemical substances or radioactive materials, and understanding their formation and development processes is essential for predicting associated damage. Consequently, numerous studies have been conducted on this phenomenon. Recently, numerical simulations investigating the mushroom cloud and the precipitation area of the so-called “black rain” following the Hiroshima atomic bombing have been reported by the Ministry of Health, Labour and Welfare of Japan. Building on the modeling framework developed in these previous studies, which accounted for hazardous bomb-derived solid-phase materials and near-surface dust, the present study performs numerical simulations of the mushroom cloud generated by the Nagasaki atomic bombing. In addition to these solid-phase components, water vapor and liquid water are included, and the phase change processes between them, together with the associated latent heat release, are taken into account. This modeling approach enables a more realistic evaluation of the temperature field within the cloud and is expected to reproduce its rising process accurately. The results show that, when latent heat release due to condensation is taken into account, the temperature inside the mushroom cloud remains high even after the initial rise, leading to a sustained buoyancy force. Consequently, the mushroom cloud ascends to a higher altitude compared with the case in which latent heat effects are neglected. In addition, the time history of the cloud-top height shows qualitative agreement with several observational datasets. These results suggest that the numerical modeling of mushroom clouds incorporating latent heat release is potentially useful for predicting the impact of hazardous substances associated with the growth of mushroom clouds.