Organelles are important subsystems of cells. The damage and inactivation of organelles are closely related to the occurrence of diseases. Organelles’ functional activity can be observed by fluorescence molecular tools. Nowadays, a series of aggregation-induced emission (AIE) bioprobes with organelles-targeting ability have emerged, showing great potential in visualizing the interactions between probes and different organelles. Among them, AIE luminogen (AIEgen)-based peptide bioprobes have attracted more and more attention from researchers due to their good biocompatibility and photostability and abundant diversity. In this review, we summarize the progress of AIEgen-peptide bioprobes in targeting organelles, including the cell membrane, nucleus, mitochondria, lysosomes and endoplasmic reticulum, in recent years. The structural characteristics and biological applications of these bioprobes are discussed, and the development prospect of this field is forecasted. It is hoped that this review will provide guidance for the development of AIEgen-peptide bioprobes at the organelles level and provide a reference for related biomedical research.