Light-induced charge separation in an organic photovoltaic (OPV) composite DTS(FBTTh2)2:PC71BM was studied. DTS(FBTTh2)2 or DTS is a non-polymer electron donor and PC71BM is a fullerene-based electron acceptor. Electron spin echo (ESE) technique has been developed to separate the signal of interfacial charge transfer state (CTS) from that of trapped charges. Pronounced out-of-phase ESE signal was observed within first few microseconds after a laser flash exciting the composite at cryogenic temperatures. This implies correlation of unpaired electron spins of DTS+ and PC71BM– species constituting CTS. The distribution of distances between these species is derived from out-of-phase ESE envelope modulation (ESEEM). Out-of-phase ESEEM traces were numerically simulated by the model assuming both magnetic dipolar and electron–hole exchange interactions within CTS. The most probable distance between DTS+ and PC71BM– within CTS increases from 4.9 nm and 5.7 nm with delays after the laser flash increase from 200 ns to 30 µs at the lowest temperature studied 20 K. This is caused by faster recombination of CTS with shorter electron–hole distance. The electron–hole exchange interaction is about J/h = 1.15 MHz for the smallest interspin distance obtained r0 = 2.5 nm. The overall similarity of the initial electron–hole distance and CTS recombination rate for DTS:PC71BM and polymer/fullerene OPV composites studied previously points to similar photoinduced charge separation mechanisms for these systems.