The low utilization of visible light and easy recombination of charge carriers of graphitic carbon nitride (CN) restrain its application as photo-electron donor and metal site support in photo-Fenton system. Herein, a hydrogen bond-induced supramolecular self-assembly strategy was created to fabricate an ultra-dispersed Cu-loaded porous tubular CN composite (CA-Cu/TCN) by the hydrothermal–pyrolysis method with citric acid (CA) as initiator and chelating agent. CA-Cu/TCN with rich nitrogen vacancies (NVs) and abundant ultra-dispersed CuNx sites exhibited narrow bandgap, favorable visible light absorption capability, and high separation and transfer efficiency of charge carriers. CA-Cu/TCN effectively catalyzed the activation of H2O2 for generating abundant reactive oxygen species under visible light irradiation, contributing to efficient degradation of ciprofloxacin (CIP) with removal rate of 95.9 % and kinetic rate constant of 0.0948 min−1. The superior catalytic activity of CA-Cu/TCN can be ascribed to the effective transport of photogenerated electrons, high specific surface area, atomically dispersed Cu species, and enriched surface NVs. The mechanism of photo-Fenton catalytic degradation of CIP and possible degradation pathways were proposed as the dominant role of 1O2. Toxicity evaluation of CIP and intermediates indicated that the degradation of CIP was a gradual detoxification process. This work offers a novel self-assembly strategy to design and synthesize highly active and sustainable visible light-driven photo-Fenton catalysts for effectively degrading organic pollutants.