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The rhesus macaque (Macaca mulatta) is a crucial experimental animal that shares many genetic, brain organizational, and behavioral characteristics with humans. A macaque brain atlas that identifies anatomically and functionally distinct regions is fundamental to biomedical and evolutionary research. However, even though connectivity information is vital for understanding brain functions, a connectivity-based whole-brain atlas of the macaque has not previously been made. In this study, we created a new whole-brain map, the Macaque Brainnetome Atlas, based on the anatomical connectivity profile provided by high-resolution angular and spatial diffusion MRI data. The new atlas consists of 248 cortical and 56 subcortical regions as well as their structural and resting-state functional connections. We systematically evaluated the parcellations and connections using multi-site and multi-modal datasets to ensure reproducibility and reliability. The resulting resource, which is downloadable fromhttp://atlas.brainnetome.org, includes (1) the thoroughly delineated Macaque Brainnetome Atlas (MacBNA), (2) the multi-modal connections, (3) the largest postmortem high resolution macaque dMRI dataset, and (4) ex vivo MRI, block-face, and Nissl-stained images obtained from a different macaque. We provide an exemplar use of the resource with a joint multi-modal and multi-scale utilization of MRI and Nissl data with our atlas as a reference system. The goals of the resource are not only to provide a backbone of the mesoscopic connectivity and a multi-omics (such as transcriptomes and proteomes) atlas but also to facilitate translational medicine, cross-species comparisons, and computational modelling, enriching the collaborative resource platform of nonhuman primate data.