We simultaneously employed grazing incidence small-angle and wide-angle X-ray scattering (GISAXS and GIWAXS) techniques to quantitatively study the structural evolution and kinetic behavior of poly(3-hexylthiophene) (P3HT) crystallization, [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) aggregation and amorphous P3HT/PCBM domains from a bulk heterojunction (BHJ) to a thermally unstable structure. The independent phase separation regimes on the nanoscale (∼10 nm), mesoscale (∼100 nm) and macroscale (∼μm) are revealed for the first time. Bis-PCBM molecules as inhibitors incorporated into the P3HT/PCBM blend films were adopted as a case study of a control strategy for improving the thermal stability of P3HT/PCBM solar cell. The detailed information on the formation, growth, transformation and mutual interaction between different phases during the hierarchical structural evolution of P3HT/PCBM:xbis-PCBM (x = 8-100%) blend films are presented herein. This systematic study proposes the mechanisms of thermal instability for a polymer/fullerene-based solar cell. We demonstrate a new fundamental concept that the structural evolution and thermal stability of mesoscale amorphous P3HT/PCBM domains during heating are the origin of controlling thermal instability rather than those of nanoscale thermally-stable BHJ structures. It leads to a low-cost and easy-fabrication control strategy for effectively tailoring the hierarchical morphology against thermal instability from molecular to macro scales. The optimum treatment achieving high thermal stability, control of mesoscale domains, can be effectively designed. It is independent of the original BHJ nanostructure design of a polymer/fullerene-based solar cell with high performance. It advances the general knowledge on the thermal instability directly arising from the nanoscale structure.