In this work, flexible 3D Co₃O₄@MnO₂ heterostructures have been successfully obtained without using any surfactants. The as-prepared flexible electrodes exhibit high efficiency, high discharge areal capacitance (1397.2 mF cm⁻² at 1 mA cm⁻²), long cycle life (13.9% loss after 6000 repetitive cycles at 1 mA cm⁻²) and excellent electrical stability. In addition, hybrid 3D Co₃O₄@MnO₂ structures are also used as photocatalysts for the photocatalytic degradation of several harmful organic dyes under visible light illumination. The results show that the as-grown products possess excellent photocatalytic performance, demonstrating their potential applications in wastewater treatment.