A study of spatio‐temporal variability of the properties of mesoscale convective systems (MCSs) is carried out during 1998–2012 over a complex terrain (20°–30°N; 80°–100°E). The regions of the maximum population and the most intense MCSs are not associated with the maximum rainfall. The deepest MCSs are not necessarily the most intense and they are predominantly found during monsoon seasons. The most intense MCSs are found during pre‐monsoon over the region A (the plains of Gangetic West Bengal, Bangladesh and Chota Nagpur Plateau) with significant reduction in intensity in monsoon. Region B (the eastern Himalaya foothills and Pegu Yoma highland) consists of relatively weak MCSs with marginal changes in their intensity from pre‐monsoon to monsoon. There is a longitudinal shift in the position of the most intense MCSs during pre‐monsoon to monsoon. Region A is associated with larger ice effective radius and ice water content in the mixed phase region compared to Region B, with significantly higher values during pre‐monsoon. During pre‐monsoon, MCSs over the regions A and B have continental and marine characteristics, respectively, whereas during monsoon both the regions have marine characteristics. There is an increasing trend in precipitation height over both the regions. For population as well as intensity, there is a contrast trend between regions A (decreasing) and B (increasing), which is supported by the trend of convective available potential energy (CAPE). During pre‐monsoon (monsoon) season, region A is associated with moderate (moderate) value of CAPE and high (low) values of wind shear; Whereas region B is associated with low (moderate) CAPE and high (low) values of wind shear. Overall significant spatio‐temporal variability in the properties of MCSs is observed, which is associated with distinctly different thermodynamical, dynamical and microphysical processes.