The thermal energy needed for the development of hurricanes and monsoons as well as any prolonged marine weather event comes from layers in the upper oceans, not just from the thin layer represented by sea surface temperature alone. Ocean layers have different modes of thermal energy variability because of the different time scales of ocean–atmosphere interaction. Although many previous studies have focused on the influence of upper ocean heat content (OHC) on tropical cyclones and monsoons, no study thus far—particularly in the North Indian Ocean (NIO)—has specifically concluded the types of dominant modes in different layers of the ocean. In this study, we examined the dominant modes of variability of OHC of seven layers in the NIO during 1998–2014. We conclude that the thermal variability in the top 50 m of the ocean had statistically significant semiannual and annual modes of variability, while the deeper layers had the annual mode alone. Time series of OHC for the top four layers were analyzed separately for the NIO, Arabian Sea, and Bay of Bengal. For the surface to 50 m layer, the lowest and the highest values of OHC were present in January and May every year, respectively, which was mainly caused by the solar radiation cycle.