Computed tomography (CT) has been used worldwide as a non-invasive test to assist in diagnosis. However, the ionizing nature of X-ray exposure raises concerns about potential health risks such as cancer. The desire for lower radiation doses has driven researchers to improve reconstruction quality. Although previous studies on low-dose computed tomography (LDCT) denoising have demonstrated the effectiveness of learning-based methods, most were developed on the simulated data. However, the real-world scenario differs significantly from the simulation domain, especially when using the multi-slice spiral scanner geometry. This paper proposes a two-stage method for the commercially available multi-slice spiral CT scanners that better exploits the complete reconstruction pipeline for LDCT denoising across different domains. Our approach makes good use of the high redundancy of multi-slice projections and the volumetric reconstructions while leveraging the over-smoothing issue in conventional cascaded frameworks caused by aggressive denoising. The dedicated design also provides a more explicit interpretation of the data flow. Extensive experiments on various datasets showed that the proposed method could remove up to 70% of noise without compromised spatial resolution, while subjective evaluations by two experienced radiologists further supported its superior performance against state-of-the-art methods in clinical practice. Code is available at https://github.com/YCL92/TMD-LDCT.