In this study, a signal-on photoelectrochemical (PEC) aptasensor for the ultrasensitive determination of kanamycin (KANA) was constructed using WO3/CdS heterojunction as photoactive material. Firstly, WO3/CdS heterojunction with excellent photoelectric response was successfully prepared by simple co-precipitation method, resulting in a strong and stable initial photocurrent. In addition, amino modified aptamers were immobilized on the electrode surface by glutaraldehyde as biological recognition components. In the presence of the target KANA, it is specifically recognized and captured by the aptamers. More importantly, KANA can act as a signal amplifier to enhance the photocurrent due to the oxidation of KANA by photogenerated holes. Therefore, a signal-on PEC aptasensor based on WO3/CdS heterojunction with high selectivity was obtained for the detection of KANA. Under optimized experimental conditions, the PEC aptasensor demonstrated a wide linear range of 10 pM to 400 nM, with a detection limit of 6.77 pM. Meanwhile, the designed PEC aptasensor had been successfully utilized for the analytical examination of milk, fish, serum, and water samples.