The structural effect of a side chain in a fullerene derivative on electron relaxation and polaronic charge transfer in a poly(3-hexylthiophene)/fullerene composite was studied by 3 cm waveband electron paramagnetic resonance. All the systems with different fullerene derivatives demonstrate a sum spectrum of small localized and mobile polarons whose contributions depend on the structure of the fullerene derivative. Both the spin–lattice and spin–spin relaxation times were determined separately in a wide (77–320 K) temperature region using the steady-state saturation method. It was shown that spin relaxation, susceptibility and dynamics are governed by the dipole–dipole interaction of the polarons as well as by the structure of the side chains in the fullerene derivative. The treatment of the polymer matrix by the fullerene changes its dimensionality and accelerates polaron diffusion along polymer chains.