Abstract This paper investigates the vertical structure of warm-cloud microphysical properties using a three-dimensional (3D) spectral bin microphysical model. A time series of contoured frequency by optical depth diagrams (CFODDs), which were proposed by previous studies, are calculated for the first time by a 3D model assuming two types of aerosol conditions (i.e., polluted and pristine). This contrasts with previous studies that obtained CFODDs using either a two-dimensional model or an accumulation of monthly and global observation data. The results show that the simulated CFODDs are characterized by distinctive patterns of radar reflectivities, similar to the patterns often observed by satellite remote sensing, even though the calculation domain of this study is limited to an area of 30 × 30 km2, whereas the satellite observations are of a global scale. A cloud microphysical box model is then applied to the simulated cloud field at each time step to identify the dominant process for each of the patterns. The results reveal that the wide variety of satellite-observed CFODD patterns can be attributed to different microphysical processes occurring in multiple cloud cells at various stages of the cloud life cycle.