molecules in a selection of compatible solvents. However, complexity in the control of BHJ thin film morphology at a molecular level is still a major bottleneck toward technological maturity mainly due to intricate intermolecular interactions [2] and large selection of organic molecules. [3] Desired BHJ morphology should possess a well-mixed nanoscale domain of moieties (for efficient dissociation of photogenerated excitons) and pure domains of each moiety (for efficient charge transport to respective electrodes) forming a bicontinuous pathway throughout the layer. [4] Difficulty lies in the optimization of each of these domains for maximum device performance. Choices of compatible molecules, blend ratio, substrate, and interlayers together with solvent formulations, additives, thermal/solvent annealing, and film drying techniques are many different variables and processes that can be utilized to create desired BHJ morphology for high efficiencies. [4,5] Additional processing steps (thermal/ solvent annealing or additives) during device fabrication for morphology optimizations is known to be beneficial to maximize efficiency. [6] However, such additional processing steps can have major influence in device operational stability. Likewise, BHJ phase morphology is vulnerable to external stresses including temperature, light, humidity, and oxygen. [7] Moreover, molecular incompatibility is one of the limiting factors of stability due to the intrinsic nature of organic materials to de-mix. In fact, spinodal de-mixing [8] has been shown to be responsible for Controlling initial bulk-heterojunction (BHJ) morphology of photoactive layer is critical for device efficiency of organic photovoltaic (OPV) cells. However, its impact on performance, specifically long-term operational stability is still poorly understood. This is mainly due to limitations in direct measurements enabling in situ monitoring of devices at a molecular level. Here, a thermal annealing preconditioning step is utilized to tune initial morphology of model polymer:fullerene BHJ OPV devices and molecular resonant vibrational spectroscopy to identify in situ degradation pathways. Direct spectroscopic evidence is reported for molecular-scale phasesegregation temperature (T PS ) which critically determines a boundary in high efficiency and long operational stability. Under operation, initially well-mixed blend morphology (no annealing) shows interface instability related to the hole-extracting layer via de-doping. Likewise, initially phasesegregated morphology at a molecular level (annealed above T PS ) shows instability in the photoactive layer via continuous phase-segregation between polymer and fullerenes in macroscales, coupled with further fullerene photodegradation. The results confirm that a thermal annealing preconditioning step is essential to stabilize the BHJ morphology; in particular annealing below T PS is critical for improved operational stability while maintaining high efficiency.