In the present study, we examine the responses of South Asian Monsoon (SAM) rainfall at intra-seasonal scale to remote dust emissions from west Asia, Tibetan Plateau and local dust emissions from within south Asia using a state of the art coupled atmosphere-slab ocean model CESM1-SOM. A series of systematically designed idealized simulations are carried out in such a way that dust emissions from the selected source regions are either perpetually suppressed or enhanced from these source regions and the response of the intra-seasonal oscillations (ISOs) of SAM rainfall to such perturbations in dust emissions are investigated. It is noted that the intra-seasonal variability of SAM rainfall is dominated by three different ISOs with periodicities of 10–20 days, 30–60 days and 60–90 days. Modulations in the characteristics of each of these three ISOs are studied for each of the dust perturbation experiments. Statistically robust K–S test and F test performed on the results from various dust perturbation experiments suggest that the perpetual perturbations in dust emissions from remote sources as well as locally from south Asia can significantly modulate the spatial and temporal structure of the ISOs of rainfall across scales during the monsoon season. Substantial changes are also noted in the spatial scales and propagation characteristics of ISOs attributable to the dust emission changes made over local and remote source regions in our idealized simulations. Our results suggest that perturbations in dust emissions over remote locations can substantially modulate the depth and duration of active and break rainfall events in the south Asian monsoon region. Results presented here have implications for better understanding and predicting the SAM rainfall variability at the intra-seasonal scales or at shorter time scales (~less than a season) under variable dust emissions from remote and local source regions.