A complex convective cloud with a horizontal scale area of more than 100 km, known as the mesoscale convective system (MCS), is important to the study as it brings heavy rainfall from its activity. The analysis of MCS with the flood-producing storm on the Indonesian Maritime Continent (IMC) receives less attention. The purpose of this study is to identify and evaluate the temporal variability of the MCS to the frequency of flood-producing storms in Greater Jakarta (GJ) during the 2013–2015 wet season. The image data of Multi-functional Transport Satellite (MTSAT) -1R, which represents an equivalent blackbody temperature (TBB), and the tracking algorithm “Grab ‘em Tag ‘em Graph ‘em” (GTG) were used to detect the events of MCS. We also used a rainfall graph in this analysis to measure rainfall threshold values in order to classify flood-producing storms. The results show that MCS around GJ has typical characteristics of tropical belt regions. There is a small TBB scale (maximum size ≥13,000 km2) distinguished by a deep cloud up to 14 km in height. Through the active effects of monsoon and ITCZ, the land-breeze and/or sea-breeze circulations that contribute to MCS growth are triggered. However, about 32 percent of the MCS contributed to the flood-producing storm around the GJ region.