Fluorescence　(FL)　imaging　and　photodynamic　therapy　(PDT)　are　popular　in　the　diagnosis　and　treatment　of　diseases,　respectively,　especially　in　cancer.　The　excitation　of　the　laser　in　the　second　near-infrared　(NIR-II)　window　can　effectively　avoid　the　interference　of　spontaneous　fluorescence　and　light　scattering　of　tissues,　obtaining　high-resolution　images　at　deeper　penetration　depth.　Due　to　their　ideal　spectral　absorbance　and　high　conversion　efficiency,　nanomaterials　with　emission　at　NIR-II　window　not　only　overcome　the　absorption　or　emission　of　NIR-II　light　by　endogenous　biomolecules,　but　also　facilitate　NIR-II　FL　imaging　and　the　application　of　photodynamic　therapy　(PDT).　The　research　progress　of　NIR-II　nanomaterials　for　FL　imaging　and　PDT　in　recent　years　is　reviewed.　First,　the　NIR-II　FL　imaging　of　several　representative　organic　and　inorganic　materials　is　introduced,　including　their　remarkable　properties　and　synthesis　methods.　Then,　the　use　of　NIR-II　nanomaterials　in　PDT,　such　as　NIR-II　FL　imaging-guided　PDT,　and　PDT　combined　with　photothermal　therapy　is　described.　Finally,　some　critical　challenges　and　open　problems　are　proposed　that　need　to　be　addressed　in　synthetic　technology　and　clinical　application.　©　2021　Wiley-VCH　GmbH