We illustrate the influence of the dipeptide structure on photosensitive damage and the kinetic mechanism was investigated using acenaphthenequinone (ACQ) as a triplet photosensitizer. With tyrosine (Tyr) serving as the core structure, two classic dipeptides with double (trptophan-tyrosine, Trp-Tyr) and single (tyrosine-alanine, Tyr-Ala and Ala-Tyr) active reaction sites were constructed, and the underlying photodamage mechanisms were investigated carefully. According to the experimental results, the proton-coupled electron transfer processes between ACQ and numerous Trp-Tyr reaction sites have independent reaction properties. The bimolecular quenching rate (kq) value is roughly equivalent to the sum of the rates of two amino acid monomers, and a novel intramolecular dynamic channel between Trp/N˙-Tyr and Trp-Tyr/O˙ was observed. The ACQ/Tyr-Ala system demonstrated the key role of steric hindrance on the kq in bimolecular reactions.