Abstract Owing to its profound influences on global energy balance, accurate representation of low cloud variability in climate models is an urgent need for future climate projection. In the present study, marine low cloud variability on intraseasonal time scales is characterized, with a particular focus over the Pacific basin during boreal summer and its association with the dominant mode of tropical intraseasonal variability (TISV) over the eastern Pacific (EPAC) intertropical convergence zone (ITCZ). Analyses indicate that, when anomalous TISV convection is enhanced over the elongated EPAC ITCZ, reduction of low cloud fraction (LCF) is evident over a vast area of the central North Pacific. Subsequently, when the enhanced TISV convection migrates to the northern part of the EPAC warm pool, a “comma shaped” pattern of reduced LCF prevails over the subtropical North Pacific, along with a pronounced reduction of LCF present over the southeast Pacific (SEPAC). Further analyses indicate that surface latent heat fluxes and boundary heights induced by anomalous low-level circulation through temperature advection and changes of total wind speed, as well as midlevel vertical velocity associated with the EPAC TISV, could be the most prominent factors in regulating the intraseasonal variability of LCF over the North Pacific. For the SEPAC, temperature anomalies at the top of the boundary inversion layer between 850 and 800 hPa play a critical role in the local LCF intraseasonal variations. Results presented in this study provide not only improved understanding of variability of marine low clouds and the underlying physics, but also a prominent benchmark in constraining and evaluating the representation of low clouds in climate models.