The effects of the high-frequency variability on the large-scale, including the intraseasonal oscillation (ISO) over the Maritime Continent (MC), is quantified using the global nonhydrostatic simulation datasets that marginally resolve mesoscale convective systems. Moisture budgets during the 2015 and 2017 boreal winter field campaign periods are analyzed. ISO events developed over the MC in both years. The period mean profiles over the MC showed upward transport of moisture by the high-frequency variability, which was of comparable to that by the low-frequency component. The high-frequency variability redistributed the bottom-heavy moistening by the low-frequency component on average. In the 2015 case, where convection was stagnant over the Indian Ocean before the ISO development under a peak El Niño condition, the high-frequency transport of moisture in the lower to middle troposphere was pronounced over land, while that over ocean was suppressed until a week before the ISO amplification. After the ISO development, high-frequency transport of moisture immediately turned to strong drying in the lower troposphere over land, while that over ocean was more synchronized with the ISO. In the 2017 case, when the MC was convectively active under a La Niña condition, the high-frequency transport of moisture over ocean was stronger than that in 2015 by a factor of 1.5, while that over land was nearly the same. These results suggest that relationship between the ISO and high-frequency variability is different over land and ocean and that depends on the environmental conditions, such as the SST distribution.