Afterglow imaging that detects photons after cessation of optical excitation avoids tissue autofluorescence and thus possesses higher sensitivity than traditional fluorescence imaging. Purely organic molecules with room‐temperature phosphorescence (RTP) have emerged as a new library of benign afterglow agents. However, most RTP luminogens only emit visible light with shallow tissue penetration, constraining their in vivo applications. This study presents an organic RTP nanoprobe (mTPA‐N) with emission in the NIR range for in vivo afterglow imaging. Such a probe is composed of RTP molecule (mTPA) as the phosphorescent generator and an NIR‐fluorescent dye as the energy acceptor to enable room‐temperature phosphorescence resonance energy transfer (RT‐PRET), ultimately resulting in redshifted phosphorescent emission at 780 nm. Because of the elimination of background noise and redshifted afterglow luminescence in a biologically transparent window, mTPA‐N permits imaging of lymph nodes in living mice with a high signal‐to‐noise ratio. This study thus opens up a universal approach to develop organic RTP luminogens into NIR afterglow imaging agents via construction of RT‐PRET. Phosphorescence resonance energy transfer is introduced to transfer the short‐wavelength emission of organic room‐temperature phosphorescence luminogens to near‐infrared fluorescent luminogens for realization of near‐infrared afterglow in vivo imaging. The doped nanoparticles of mTPA‐N are applied for subcutaneous and lymph‐node imaging in living mice with extremely low background noise and deep tissue penetration.