Through comprehensive density functional theory calculations, the photodegradation mechanisms, including cis–trans isomerization, electrocyclization, and sigmatropic rearrangement reactions are investigated in indacenodithieno [3,2‐b] thiophene (IT)‐based non‐fullerene acceptors (NFAs). Various functional group substitutions on the core (fluorine, ethyl, and cyano groups) and end groups (fluorine) of NFA are introduced to elucidate the influence of chemical modifications on photodegradation pathways. The findings reveal that the core substitution can effectively suppress electrocyclization and 1,5‐sigmatropic shift reactions, which are major contributors to photodegradation. Furthermore, the electronic, excited‐state, and charge transport properties of pristine and degraded products are studied to gain insights into the impact of degradation on photovoltaic parameters. The results suggest that photodegradation leads to the formation of shallow energy trap states, hindering charge transport and increasing charge recombination, ultimately affecting the power conversion efficiency of organic solar cells (OSCs). The study not only provides a comprehensive understanding of photodegradation mechanisms but also offers valuable molecular design strategies to enhance the stability of NFAs for future large‐scale applications of OSCs. By establishing a clear connection between the chemical structure and photostability of NFA, this research represents a pivotal contribution to the field of organic electronics and sustainable energy technologies.