Cranial nerves (CNs) play a crucial role in various essential functions of the human brain, and mapping their pathways from diffusion MRI (dMRI) provides valuable preoperative insights into the spatial relationships between individual CNs and key tissues. However, mapping a comprehensive and detailed CN atlas is challenging because of the unique anatomical structures of each CN pair and the complexity of the skull base environment.In this work, we present what we believe to be the first study to develop a comprehensive diffusion tractography atlas for automated mapping of CN pathways in the human brain. The CN atlas is generated by fiber clustering by using the streamlines generated by multi-parametric fiber tractography for each pair of CNs. Instead of disposable clustering, we explore a new strategy of multi-stage fiber clustering for multiple analysis of approximately 1,000,000 streamlines generated from the 50 subjects from the Human Connectome Project (HCP). Quantitative and visual experiments demonstrate that our CN atlas achieves high spatial correspondence with expert manual annotations on multiple acquisition sites, including the HCP dataset, the Multi-shell Diffusion MRI (MDM) dataset and two clinical cases of pituitary adenoma patients. The proposed CN atlas can automatically identify 8 fiber bundles associated with 5 pairs of CNs, including the optic nerve CN II, oculomotor nerve CN III, trigeminal nerve CN V and facial-vestibulocochlear nerve CN VII/VIII, and its robustness is demonstrated experimentally. This work contributes to the field of diffusion imaging by facilitating more efficient and automated mapping the pathways of multiple pairs of CNs, thereby enhancing the analysis and understanding of complex brain structures through visualization of their spatial relationships with nearby anatomy.