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The production of a radical cation-containing covalent organic framework (COF) has been accomplished by sequential in situ reactions, quaternization, and one-electron reduction of the 2,2′-bipyridine-based COFs. The acid-catalyzed COF formation enables the cis configuration of 2,2′-bipyridyl moieties in the structure, of which the stability arises from the eclipsed stacking of the two-dimensional layered structure. The postfunctionalization generates cyclic alkylated diquats as the sole products from the controlled quaternization. The reduction of diquat cations on the COF skeletons results in a large number of radical cations, which delocalize and uniaxially stack on top of one another by virtue of interlayered π-electronic couplings. The absorption of the near-infrared (NIR) region exhibited by the cationic radical COF is remarkably high owing to the intercharge transfer across the π-coupling interlayers. Also, the long-range array of extended and planar frameworks in such a COF leads to the extra stability of the radical cations against external stresses. The structure-enhanced performance of the COF material is witnessed with photothermal conversion efficiencies of as high as 63.8 and 55.2% when exposed to 808 and 1064 nm lasers, respectively. Further PEG modification on such a COF allows photoacoustic imaging and photothermal therapy in vivo under NIR light illumination to be manifested.