In recent years, the frequent eutrophication of water bodies around the world has led to the accumulation of microcystins (MC-LR) in water bodies, causing great harm to humans and aquatic organisms. In this study, a Z-scheme Ag3PO4/NG/PI composite photocatalyst was fabricated by using silver orthophosphate, nitrogen-doped graphene and polyimide for photocatalytic degradation of MC-LR under visible light irradiation. The structure, morphology and optical properties of Ag3PO4/NG/PI were characterized by XRD, SEM, TEM, XPS, FT-IR, BET, and UV-vis DRS. The degradation ratio of MC-LR by Ag3PO4/NG/PI photocatalysts was higher (up to 94.4%) than that of pure Ag3PO4 for MC-LR degradation within 10 h under visible light irradiation, and the kinetic constant over Ag3PO4/NG/PI was similar to 7 times of pure Ag3PO4. Based on the results of Liquid Chromatography-Mass Spectrometry (LC-MS), the possible degradation pathways of MC-LR were proposed. Photoelectrochemistry measurement (the photocurrent response, electrochemical impedance spectroscopy and Mott-Schottky plots), radical trapping experiment, electron spin resonance test, PL spectroscopy and analysis of band gap have revealed that the photocatalysis of Ag3PO4/NG/PI follows the Z-scheme mechanism, which can not only promote the separation and migration of photogenerated carriers to reduce re-combination, but also maintain a strong redox capacity. Meanwhile, the stability of Ag3PO4/NG/PI photocatalyst is greatly improved because the photogenerated electrons (e(-)) of Ag3PO4 are migrated to NG to suppress the photo-corrosion of Ag3PO4.