<p>Inter-annual variability of clouds is important for understanding climate feedback. This study examines how the anomalous positioning of the subtropical high influences large-scale circulation patterns linked to Indian Ocean Dipole (IOD) and El Niño-Southern Oscillation (ENSO), and how these dynamical changes govern the interannual variability of cloud cover over the Indian Ocean. In this paper, monthly ERA5 reanalysis datasets were used for the period 1979 to 2018. Results indicate that during the positive phases of IOD and ENSO, cloud fraction increases over the western Indian Ocean and decreases over the eastern side, forming a dipole pattern. In contrast, the negative phases are associated with an overall increase in cloud fraction across the basin. These findings offer novel insights, as the influence of IOD and ENSO on cloud fraction over the Indian Ocean has been largely unexplored. The study found that during the positive phases of IOD and ENSO, the subtropical high shifts toward the southeastern Indian Ocean, inducing divergent winds and strengthening easterlies that transport moisture from east to west, thereby increasing cloud fraction over the western Indian Ocean. The combined influence of IOD and ENSO on cloud fraction variability is both season- and cloud-type-dependent. Their impact is strongest during the JJA and SON seasons, explaining up to 27–29% of the variance, while it remains limited during DJF (notably only mid-level clouds) and only 4–12% in MAM. The study provides new insights into the role of IOD, ENSO, and subtropical high in explaining the inter-annual variability of clouds by modulating the large-scale circulations and moisture transport over the Indian Ocean. It contributes to a better understanding of cloud-radiative feedbacks and their implications for regional climate variability.</p>