Accurate whole-heart segmentation is a critical component in the precise diagnosis and interventional planning of cardiovascular diseases. Integrating complementary information from modalities such as computed tomography (CT) and magnetic resonance imaging (MRI) can significantly enhance segmentation accuracy and robustness. However, existing multi-modal segmentation methods face several limitations: severe spatial inconsistency between modalities hinders effective feature fusion; fusion strategies are often static and lack adaptability; and the processes of feature alignment and segmentation are decoupled and inefficient. To address these challenges, we propose a dual-branch U-Net architecture enhanced by reinforcement learning for feature alignment, termed RL-U$^2$Net, designed for precise and efficient multi-modal 3D whole-heart segmentation. The model employs a dual-branch U-shaped network to process CT and MRI patches in parallel, and introduces a novel RL-XAlign module between the encoders. The module employs a cross‑modal attention mechanism to capture semantic correspondences between modalities and a reinforcement‑learning agent learns an optimal rotation strategy that consistently aligns anatomical pose and texture features. The aligned features are then reconstructed through their respective decoders. Finally, an ensemble‑learning–based decision module integrates the predictions from individual patches to produce the final segmentation result. Experimental results on the publicly available MM-WHS 2017 dataset demonstrate that the proposed RL-U$^2$Net outperforms existing state-of-the-art methods, achieving Dice coefficients of 93.1\% on CT and 87.0\% on MRI, thereby validating the effectiveness and superiority of the proposed approach.