In this work, a novel visible light-driven self-powered photoelectrochemical (PEC) platform was designed based on 3D N-doped graphene hydrogel/hematite nanocomposites (NGH/Fe2O3) via a facile one-pot hydrothermal route. The coupling NGH with Fe2O3 could generate a Schottky junction, which promoted the separation of charges. Moreover, Mott-Schottky measurements validated that the carrier concentration achieved by NGH/Fe2O3 was about 3.4 × 103 times in comparison to that of pure Fe2O3, which was beneficial for efficient charge transfer. Owing to the carrier density effect and Schottky junction, the photocurrent of the as-fabricated NGH/Fe2O3 nanocomposites was 6.9-fold higher than that of pure Fe2O3. On the basis of such excellent Schottky junctions, an ultrasensitive visible light-induced self-powered PEC aptasensor was developed using a Microcystin-LR (MC-LR) aptamer. The as-fabricated PEC aptasensor displayed good analytical performance toward MC-LR detection in terms of wide linear range (1 pM-5 nM), low detection limit (0.23 pM, S/N = 3), excellent selectivity and high stability. This new strategy can provide a way for regulating nanostructures for more sensitive PEC sensors by increasing the carrier density.