Direct neural inputs to immune organs have been observed for decades, with their functions in neuroimmune regulation being increasingly appreciated. However, the current knowledge of such neural structures, particularly those in primate immune organs, remains incomplete. In this study, we comprehensively assessed the 3D anatomy of autonomic (i.e., sympathetic and parasympathetic) innervations in the immune organs of the rhesus macaque monkey and the human for the first time. Aided with the advanced technique of whole-tissue immunolabeling and lightsheet fluorescence imaging, we revealed the densely organized sympathetic architecture in the parenchyma of the adult monkey and human spleens. On the other hand, only sparse, if any, sympathetic inputs were observed inside the lymph nodes, Peyer's patches, or thymus. In contrast, there were minimal parasympathetic innervations in the parenchyma of these examined immune organs. Together, this work has documented the unique patterns of autonomic innervations in different immune organs of a non-human primate and the human, serving as an essential reference for future research on neuroimmune regulation in the field.