Controllable　self-assembly　of　photonic　molecules　for　precise　biomedicine　is　highly　desirable　but　challenging　to　prepare　multifunctional　nano-phototheranostics.　Herein,　we　developed　a　generic　self-assembly　approach　to　design　nano-phototheranostics　that　provides　NIR-II　fluorescence　imaging　and　phototherapy.　We　first　designed　and　synthesized　two　amphiphilic　photonic　molecules,　PEG(2000)-IR806　and　BODIPY.　Then,　we　prepared　the　co-self-assembled　phototheranostic　agents,　PEG(2000)-IR806/B　ODIPY　nanoparticles　(PIBY　NPs).　The　morphology　of　the　PIBY　NPs　is　controllable　by　adjusting　the　ratio　of　PEG(2000)-IR806　and　BODIPY　during　self-assembly.　The　NIR-II　fluorescence　properties　and　phototherapy　capability　of　the　PIBY　NPs　were　demonstrated　in　vitro　and　in　vivo　.　By　tuning　the　ratio　of　PEG(2000)-IR806　and　BODIPY,　the　PIBY　NPs　showed　various　morphologies　(e.g.　spherical　nanoparticles,　nanovesicles　and　rod-like　nanoparticles).　The　PEG(2000)-IR806　plays　two　roles　in　the　co-self-assemblies,　one　is　second　near-infrared　(NIR-II,　1000-1700　nm)　agent,　the　other　is　the　surfactant　for　BODIPY　encapsulation.　The　phototherapeutic　PIBY　NPs　all　show　bright　NIRII　fluorescence　and　effective　phototherapeutic　(photothermal　and　photodynamic)　properties,　which　are　attributed　to　IR806　and　BODIPY,　respectively.　The　driving　force　of　the　self-assembly　can　be　attributed　to　the　electrostatic　interaction　between　NIR806　and　BODIPY　and　their　hydrophobicity.　The　rod-like　PIBY　NPs　(rPIBY　NPs)　demonstrated　a　low　half　inhibitory　concentration　(IC50)　of　3.96　mu　g/mL　on　U87MG　cells.　The　NIR-II　imaging　showed　the　accumulation　of　rPIBY　NPs　in　the　tumor　region.　After　systemic　injection　of　rPIBY　NPs　at　low　dose　(0.5　mg/kg),　the　tumor　growth　was　greatly　inhibited　upon　laser　irradiation　without　noticeable　side　effects.　This　study　provides　a　generic　self-assembly　approach　to　fabricate　NIR-II　imaging　and　phototherapeutic　platform　for　cancer　phototheranostics.　Statement　of　significance　Nanophototheranostics　providing　NIR-II　fluorescence　imaging　and　phototherapy　are　expected　to　play　a　critical　role　in　modern　precision　medicine.　Controllable　self-assembly　of　optical　molecules　for　the　fabrication　of　efficient　nanophototheranostics　is　highly　desirable　but　challenging.　This　work　reports　for　the　first　time　the　co-assembly　of　a　NIR-II　imaging　contrast　agent　and　a　phototherapeutic　agent　to　yield　nanophototheranostics　with　various　morphologies.　The　design　of　molecular　co-assembly　with　complementary　optical　functions　can　be　a　generic　method　for　future　the　development　of　phototheranostics.　(C)　2021　Acta　Materialia　Inc.　Published　by　Elsevier　Ltd.　All　rights　reserved.