3D medical image segmentation is crucial for precision medicine, yet it faces challenges such as noise, blurred boundaries, and the balance between local and global features. This paper proposes the FSDB-Diff model, which integrates diffusion models with a 3D U-Net architecture. It features a dual-branch structure in the frequency domain and spatial domain, and incorporates high-low frequency fusion with cross-domain attention mechanisms. Experiments on the BraTS 2020 and BTCV datasets demonstrate that this method significantly outperforms current state-of-the-art approaches. The mean Dice score improves by 1.12%, while the HD95 metric decreases by 0.98. Ablation studies validate the effectiveness of each module, providing an efficient solution for clinical diagnostic assistance.