Two case studies of the mesoscale convective system (MCS) in the Indonesian region were conducted by applying an improved “Grab ‘em Tag ‘em Graph ‘em” (GTG) tracking algorithm and the Integrated Cloud Analysis System (ICAS) algorithm to Himawari-8 AHI infrared data. The first case over Java Island showed a land-originating MCS in the boreal winter, which coincided with a wet phase of Madden-Julian Oscillation (MJO) over the Maritime Continent. The second case showed the evolution of MCS under the influence of a strong vertical wind shear during the boreal summer. The cloud top height (CTH) of deep convective part in the first case was larger than that in the second case, while the temporal evolution of CTH was similar between the two cases. For the anvil part, the median CTH of the second case was relatively stable at around 13 km, while that of the first case showed a considerable temporal variation ranging from 14 to 16 km. The cloud-particle effective radius (CER) of the anvil increased after the period of maximum deep convective CTH in both cases, although the CER was slightly larger in the second case than in the first case. These differences in cloud properties between the two cases were attributable to the background wind profiles.