The quest for an all‐organic nanosystem with negligible cytotoxicity and remarkable in vivo tumor theranostic capability is inescapably unending. Hitherto, the landscape of available photothermal agents is dominated by metal‐based nanoparticles (NPs) with attendant in vivo negatives. Here, an all‐organic‐composed theranostic nanosystem with outstanding biocompatibility for fluorescence image‐guided tumor photothermal therapy, and as a potential alternative to metal‐based photothermal agents is developed. This is rationally achieved by compartmentalizing indocyanine green (ICG) in glycol chitosan (GC)‐polypyrrole (PP) nanocarrier to form hybrid ICG@GC‐PP NPs (≈65 nm). The compartmentalization strategy, alongside the high photothermal conversion ability of PP jointly enhances the low photostability of free ICG. Advantageously, ICG@GC‐PP is endowed with an impeccable in vivo performance by the well‐known biocompatibility track records of its individual tri organo‐components (GC, PP, and ICG). As a proof of concept, ICG@GC‐PP NPs enables a sufficiently prolonged tumor diagnosis by fluorescence imaging up to 20 h post‐injection. Furthermore, owing to the complementary heating performances of PP and ICG, ICG@GC‐PP NPs‐treated mice by one‐time near‐infrared irradiation exhibit total tumor regression within 14 days post‐treatment. Therefore, leveraging the underlying benefits of this study will help to guide the development of new all‐organic biocompatible systems in synergism, for safer tumor theranostics.