Molecular fluorophores with the second near‐infrared (NIR‐II) emission hold great potential for deep‐tissue bioimaging owing to their excellent biocompatibility and high resolution. Recently, J‐aggregates are used to construct long‐wavelength NIR‐II emitters as their optical bands show remarkable red shifts upon forming water‐dispersible nano‐aggregates. However, their wide applications in the NIR‐II fluorescence imaging are impeded by the limited varieties of J‐type backbone and serious fluorescence quenching. Herein, a bright benzo[c]thiophene (BT) J‐aggregate fluorophore (BT6) with anti‐quenching effect is reported for highly efficient NIR‐II bioimaging and phototheranostics. The BT fluorophores are manipulated to have Stokes shift over 400 nm and aggregation‐induced emission (AIE) property for conquering the self‐quenching issue of the J‐type fluorophores. Upon forming BT6 assemblies in an aqueous environment, the absorption over 800 nm and NIR‐II emission over 1000 nm are boosted for more than 41 and 26 folds, respectively. In vivo visualization of the whole‐body blood vessel and imaging‐guided phototherapy results verify that BT6 NPs are excellent agent for NIR‐II fluorescence imaging and cancer phototheranostics. This work develops a strategy to construct bright NIR‐II J‐aggregates with precisely manipulated anti‐quenching properties for highly efficient biomedical applications.