A solution of fullerene C60 in N-methylpyrrolidone (NMP) presents a suitable system for obtaining fullerene's clusters with the tunable size. However, the mechanism of fullerenes interaction with polar NMP molecules is still elusive. Herein, we present the measured laser desorption/ionization mass spectra (LDI MS) of the precipitates produced from C60/NMP solutions of different age in comparison with the typical spectra of C60 crystallized from toluene and benzene. The distinctive characteristics of the C60/NMP mass spectra were identified and carefully examined. The number of characteristic peaks and their relative intensities in the spectra strongly depend on the age of initial C60/NMP solutions. This effect was attributed to the specific C60-NMP interactions in the solution, namely to the formation of charge-transfer complexes of C60 with NMP molecules followed by fullerene cluster formation. The results of additional measurements carried out by means of small-angle X-ray scattering (SAXS), nuclear magnetic resonance (NMR), UV–Vis absorption spectroscopy together with the density functional theory (DFT) calculations are in accord with the proposed hypothesis.