Deciphering singlet-to-triplet intersystem crossing (ISC) in organic near-infrared photosensitizers (PSs) is of fundamental importance in the designing of high-performance PSs to boost the clinical usage of photodynamic therapy (PDT). However, in-depth investigations of the ISC dynamics in near-infrared PSs have not been performed to date. Here, systematical investigations of the ISC dynamics in organic near-infrared BODIPY derivatives are presented, in which a multi-channel yet remarkably efficient ISC process is revealed by ultrafast femtosecond transient absorption (fs-TA) spectroscopy and theoretical calculation. The fs-TA verifies an exceptionally enhanced ISC efficiency (Φ ISC = 91%) in iodine-substituted BODIPY (2I-BDP) which is further supported by the calculation results. This endows 2I-BDP with an ultrahigh singlet oxygen quantum yield (Φ Δ = 88%), thus enabling a proof-of-concept application of highly efficient PDT in vivo under ultralow near-infrared light power density (10 mW cm-2). The in-depth understanding of ISC dynamics in organic near-infrared materials may provide valuable guidance in the designing of novel organic theranostic materials for clinical cancer treatment.