Cone-beam computed tomography (CBCT) is widely used in dental and maxillofacial imaging, but low-dose acquisition introduces strong, spatially varying noise that degrades soft-tissue visibility and obscures fine anatomical structures. Classical denoising methods struggle to suppress noise in CBCT while preserving edges. Although deep learning-based approaches offer high-fidelity restoration, their use in CBCT denoising is limited by the scarcity of high-resolution CBCT data for supervised training. To address this research gap, we propose a novel Hybrid Attention Residual U-Net (HARU-Net) for high-quality denoising of CBCT data, trained on a cadaver dataset of human hemimandibles acquired using a high-resolution protocol of the 3D Accuitomo 170 (J. Morita, Kyoto, Japan) CBCT system. The novel contribution of this approach is the integration of three complementary architectural components: (i) a hybrid attention transformer block (HAB) embedded within each skip connection to selectively emphasize salient anatomical features, (ii) a residual hybrid attention transformer group (RHAG) at the bottleneck to strengthen global contextual modeling and long-range feature interactions, and (iii) residual learning convolutional blocks to facilitate deeper, more stable feature extraction throughout the network. HARU-Net consistently outperforms state-of-the-art (SOTA) methods including SwinIR and Uformer, achieving the highest PSNR (37.52 dB), highest SSIM (0.9557), and lowest GMSD (0.1084). This effective and clinically reliable CBCT denoising is achieved at a computational cost significantly lower than that of the SOTA methods, offering a practical advancement toward improving diagnostic quality in low-dose CBCT imaging.