Microcystins (MCs) are produced by cyanobacteria blooms in eutrophic water and can cause acute and chronic toxicity and even mortality to animals and humans. Previous MC removal strategies concernedonly highly contaminated water, in which the concentration of the pollutant was considerably larger than that in the natural world. In this study, we developed a composite of TiO₂-coated magnetic carbon microtube (C-TiO₂-Fe₃O₄) and used it as a photocatalyst to efficiently remove microcystin-LR (MC-LR) from water under visible light from water. And the huge surface of the carbon microtube dramatically boosted the adsorbability and charge mobility, which lowered the recombination rate of electron–hole pairs, and hence systematically enhanced photocatalytic activity. The combination of adsorption and photodegradation endowed the composite with a better performance in the removal of trace amounts of MC-LR than the C-TiO₂. It was found that increasing the contact time and catalyst dosage, acidic environment, and lower initial MC-LR concentration had positive effects on MC-LR removal. The optimum reaction conditions of C-TiO₂-Fe₃O₄ was a reaction time of 12.68 min, a catalyst dosage of 0.39 g·L⁻¹, and a pH of 7.72. The C-TiO₂-Fe₃O₄ (surface area normalized apparent reaction rate constants K/S_BET = 1.2 × 10⁻⁴) presented a higher reaction rate than C-TiO₂ (K/S_BET = 8.4 × 10⁻⁵). Moreover, the stable removal capability of C-TiO₂-Fe₃O₄ was confirmed over multiple cycles. Finally, the ecological safety performance was also evaluated after visible light illumination. This work paves the way for the development of more efficient and easily separable purifiers for the removal of pollutants and toxins from contaminated water.