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,　PEG2000-IR806　and　BODIPY.　Then,　we　prepared　the　co-self-assembled　phototheranostic　agents,　PEG2000-IR806/BODIPY　nanoparticles　(PIBY　NPs).　The　morphology　of　the　PIBY　NPs　is　controllable　by　adjusting　the　ratio　of　PEG2000-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　PEG2000-IR806　and　BODIPY,　the　PIBY　NPs　showed　various　morphologies　(e.g.　spherical　nanoparticles,　nanovesicles　and　rod-like　nanoparticles).　The　PEG2000-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　NIR-II　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　µg/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.　©　2021　Acta　Materialia　Inc.