Display omitted Carbon nitride (C3N4) is a promising photocatalyst that can be applied in environmental remediation and energy conversion. However, the absorption range and charge separation efficiency of C3N4 are still severely restricted for its large-scale practical applications. Herein, we demonstrate a simple thermal polymerization and electrodeposition method, followed by partial etching strategy to synthesize direct Z-scheme porous zinc oxide/amorphous carbon nitride/manganese dioxide hybrid core-shell nanorod array (denoted as P-ZnO/ACN/MnO2) by encapsulating amorphous carbon nitride layers (ACN) and manganese dioxide nanosheets (MnO2) on the zinc oxide nanorod arrays (denoted as ZnO). Interestingly, ZnO serves as the collector of charge carriers and MnO2 plays a significant role in protecting ACN from corrosion. The as-prepared Z-scheme P-ZnO/ACN/MnO2 heterojunction exhibits high photocurrent density of 5.2 mA cm−2 at 0.6 V vs. Ag/AgCl, high photoconversion efficiency 0.98%, and universal photoelectrocatalytic degradation activity for degradation of organic dyes under visible light irradiation. The band gap energy and conduction band position of ZnO, ACN and MnO2 are calculated by UV–visible diffuse reflection and Mott-Schottky measurement, which strongly support the direct Z-scheme charge carrier migration mechanism. This finding provides an efficient strategy to construct highly active and stable C3N4-based Z-scheme photocatalytic system.