The Indian Summer Monsoon Rainfall (ISMR) contributes to 80% of India’s annual precipitation, affecting 1.4 billion people. The performance of CMIP6 models in simulating ISMR is still inadequate. Traditional dynamic or statistical downscaling techniques have only modestly improved ISMR simulations. While deep learning models like YNet have shown promise in global downscaling efforts, we found their application to ISMR has been less effective, particularly for extreme rainfall and intraseasonal variability. We developed two advanced super-resolution deep learning models to overcome these limitations: YNet_D and YNet_DE. YNet_D enhances the downscaling accuracy by integrating atmospheric variables, informed by monsoon dynamics, with coarse precipitation data as predictors. YNet_DE prioritizes extreme rainfall using a weighted loss function, effectively addressing the challenge of simulating extremes. Both models outperform YNet, with YNet_D and YNet_DE achieving root mean squared errors (RMSE) of 12.25 mm and 11.97 mm, respectively, compared to YNet’s 12.41 mm. In terms of extremes, YNet_D and YNet_DE reduced the bias in the 95th percentile (R95p) from 78.27 mm with YNet to 56.52 mm and 40.22 mm, respectively. Additionally, both models showed significant improvements in simulating ISMR’s intraseasonal and interannual variations and demonstrated strong transferability to General Circulation Models (GCMs), with YNet_DE notably lowering the multi-model mean bias for R95p from 114.3 mm in the original GCMs and 130.0 mm in YNet simulations to 64.4 mm. Unlike conventional statistical methods, these models retain the critical physical dynamics of ISMR, offering a robust solution that preserves the system’s variability and complexity.