The amplification of extreme weather events due to climate change poses serious threats to biodiversity, human health, and food security. While climate models (GCMs) are essential for predicting future climate, their low resolution and high computational costs limit their ability to represent extreme events. In this paper, we introduce FuXi-CMIPAlign, a generative deep learning framework for downscaling the output of the Coupled Model Intercomparison Project (CMIP). This model performs generative modeling using flow matching and integrates domain adaptation via the Maximum Mean Discrepancy (MMD) loss to align feature distributions between training and inference data. This mitigates input mismatch and improves accuracy, stability, and generalization across emission scenarios. FuXi-CMIPAlign performs spatial, temporal, and multivariate downscaling, enabling more realistic simulations of complex extreme events such as tropical cyclones.