Photoacoustic　imaging　(PM)　has　attracted　great　attention　in　the　diagnosis　and　treatment　of　diseases　due　to　its　noninvasive　properties.　Especially　in　the　second　near-infrared　(NIR-II)　window,　PAI　can　effectively　avoid　the　interference　of　tissue　spontaneous　fluorescence　and　light　scattering,　and　obtain　high　resolution　images　with　deeper　penetration　depth.　Because　of　its　ideal　spectral　absorption　and　high　conversion　efficiency,　NIR-II　PA　contrast　agents　overcome　the　absorption　or　emission　of　NIR-II　light　by　endogenous　biomolecules.　In　recent　years,　a　series　of　NIR-II　PA　contrast　agents　have　been　developed　to　improve　the　performance　of　PAI　in　disease　diagnosis　and　treatment.　In　this　paper,　the　research　progress　of　NIR-II　PA　contrast　agents　and　their　applications　in　biomedicine　are　reviewed.　PA　contrast　agents　are　classified　according　to　their　composition,　including　inorganic　contrast　agents,　organic　contrast　agents,　and　hybrid　organic-inorganic　contrast　agents.　The　applications　of　NIR-II　PA　contrast　agents　in　medical　imaging　are　described,　such　as　cancer　imaging,　inflammation　detection,　brain　disease　imaging,　blood　related　disease　imaging,　and　other　biomedical　application.　Finally,　the　research　prospects　and　breakthrough　of　NIR-II　PA　contrast　agents　are　discussed.