Nanoscale morphology is critical to determining the device efficiency of bulk heterojunction organic solar cells, and the ideal structure is often described as a three-phase network with one well-mixed phase for efficient charge separation and two purer phases for efficient charge transport. In order to understand such nanoscale morphology, we have performed detailed spectroscopic investigations and identified the three-phase morphology evolution in one of the classic blend systems, P3HT:PCBM. The impact of different phases on polymer molecular (chain conformational) order and blend thermal and optical properties were monitored in situ using resonant Raman, absorption, and photoluminescence spectroscopy techniques. Semicrystalline P3HT was found to accommodate up to ∼25% PCBM (by weight) in its amorphous phase, with very little impact on either polymer molecular order or aggregation. Higher concentrations of PCBM resulted in a greater proportion of amorphous mixed phase and reduced polymer molecular order and aggregation. On the other hand, the formation of crystalline purer phases via phase separation was evident during in situ thermal annealing, revealing a consistent glass transition temperature (Tg) of ∼50 °C in blends with up to 50% wt PCBM. This indicates similar local chemical compositions in the amorphous mixed phase present in blends despite different overall blend ratios. A much higher Tg (80–100 °C) was observed for blends with >50% wt PCBM, indicating a stronger impact of PCBM on P3HT molecular order and thermal properties, requiring a higher annealing temperature to ensure formation of the preferred three-phase morphology.