Radical pairs, polarons and fullerene anion radicals photoinduced by photons with energy of 1.98–2.73 eV in bulk heterojunctions formed by poly(3-hexylthiophene) (P3HT) with bis(1-[3-(methoxycarbonyl)propyl]-1-phenyl)-[6.6]C62 (bis-PCBM) methanofullerene have been studied as compared with P3HT/PCBM composite by direct light-induced EPR (LEPR) method in a wide temperature range. A part of spin polarons and methanofullerene anion radicals are pinned in trap sites which number and depth are governed by an ordering of the polymer/fullerene system and energy of initiating photons. It has been shown that dynamics and recombination of mobile polarons and counter methanofullerene anion radicals are governed by their exchange- and multi-trap assisted diffusion. Relaxation and dynamics of both the charge carriers determined by the steady-state saturation method are governed by structure and conformation of their microenvironment as well as by the photon energy. Longitudinal diffusion of polarons was shown to depend on lattice phonons of crystalline domains embedded into an amorphous polymer matrix. The energy barrier required for polaron interchain hopping is higher than its intrachain diffusion. Pseudorotation of fullerene derivatives in a polymer matrix was shown to follow the activation Pike model. The replacement of PCBM by bis-PCBM provides higher anisotropy of polaron dynamics and decreases its selectivity to the photon energy. This makes spin dynamics easier and minimizes energy dispersion at charge transfer.