As an electric current passes through an organic semiconductor, a small number of organic molecules will inevitably act as a polaron state that is similar to an ionic charged state. The continuous device operation of organic semiconducting molecules is directly associated with the stability of the charged state. Herein, we choose the high-performance Y-series of nonfullerene acceptors to investigate the stability by a spectro-electrochemical technique. The results reveal the discoloration of molecules in the charged state and can be partially recovered after neutralization with about 10% irreversible part. It is found that the degree of the irreversible process is associated with halogen substituents at the end groups, and the irreversible reactions are also discussed. Our results reveal that the stability of a charged state can be improved by the fine-tuning of the molecular structures, and the local charge density can also be rapidly reduced by the high carrier mobility, the key factor to improving the stability of nonfullerene acceptors for better practical applications.