Currently, one of important research directions of photoelectrochemical (PEC) bioanalysis is to exploit innovative photoactive species and their elegant implementations for selective detection and signal transduction. Different from existing candidates for photoelectrode development, this study, exemplified by the cationic dipeptide nanoparticles (CDNPs), reports the first demonstration of self-assembled peptide nanostructures (SAPNs) for the PEC bioanalysis. Specifically, the CDNPs were prepared as representative materials and then immobilized onto the indium tin oxide (ITO) electrode for the PEC differentiation of several commonly involved biomolecules such as ascorbic acid (AA) and l-cysteine. Significantly, the experimental results disclosed that the CDNPs possessed unique photocathodic responses and good analytical performance toward AA detection in terms of rapid response, high stability, and excellent selectivity. This work demonstrates the great potential of the large SAPN family for the future PEC bioanalysis development and has not been reported to our knowledge.