Photoactive material and recognition element are two crucial factors which determine the sensitivity and selectivity of the photoelectrochemical (PEC) sensor. Herein we developed a novel PEC aptamer sensor for the specific detection of kanamycin using water-dispersible graphite-like carbon nitride (w-g-C3N4) as visible light-active material and aptamer as the biorecognition element. While a suitable amount of graphene oxide (GO) was doped in w-g-C3N4, the visible light photocurrent response was enhanced, which was beneficial to the construction of PEC sensor. On the other hand, the large specific surface area and π-conjugated structure of GO/w-g-C3N4 provided an excellent platform for immobilizing the kanamycin-binding DNA aptamer on the surface of the sensor via π-π stacking interaction. On such a sensor, the capture of kanamycin molecules by aptamer resulted in increased photocurrent. The PEC response of the sensor was found to be linearly proportional to the concentration of kanamycin in the range from 1 nM to 230 nM with a detection limit (3S/N) of 0.2 nM. Moreover, the proposed sensor displayed high selectivity, good reproducibility, and high stability, demonstrating the successful combination of GO/w-g-C3N4 with aptamer in fabricating high performance PEC sensors.