Molecular fluorophores emitting in the second near-infrared (NIR-II, 1000-1700 nm) window with strong optical harvesting and high quantum yields hold great potential for in vivo deep-tissue bioimaging and high-resolution biosensing. Recently, J-aggregates are harnessed to engineer long-wavelength NIR-II emitters and show unique superiority in tumor detection, vessel mapping, surgical navigation, and phototheranostics due to their bathochromic-shifted optical bands in the required slip-stacked arrangement aggregation state. However, despite the preliminary progress of NIR-II J-aggregates and theoretical study of structure-property relationships, further paradigms of NIR-II J-aggregates remain scarce due to the lack of study on aggregated fluorophores with slip-stacked fashion. In this effort, how to utilize the specific molecular structure to form slip-stacked packing motifs with J-type aggregated exciton coupling is emphatically elucidated. First, several molecular regulating strategies to achieve NIR-II J-aggregates containing intermolecular interactions and external conditions are positively summarized and deeply analyzed. Then, the recent reports on J-aggregates for NIR-II bioimaging and theranostics are systematically summarized to provide a clear reference and direction for promoting the development of NIR-II organic fluorophores. Eventually, the prospective efforts on ameliorating and promoting NIR-II J-aggregates to further clinical practices are outlined.