As organic dyes are the main pollutants in water pollution, seeking effective removal solutions is urgent for humans and the environment. A novel environmentally friendly three-dimensional CoFe-LDHs (3D CoFe-LDHs) catalyst was synthesized by one-step hydrothermal method. Scanning electron microscopy, energy dispersive spectroscopy, Fourier transform infrared spectra, X-ray diffraction, X-ray photoelectron spectroscopy, Brunauer-Emmett-Teller technique as well as UV-Vis diffuse reflectance spectra were used to characterize the prepared samples. The experimental results revealed that 3D CoFe-LDHs exhibited a rapid decolorization of methyl orange and Rhodamine B by heterogeneous photo-Fenton process after reaching the adsorption equilibrium, and the final decolorization efficiency reached 91.18% and 93.56%, respectively. On the contrary, the decolorizing effect of 3D CoFe-LDHs on neutral blue was relatively weak. The initial concentrations of azo dyes, pH and H2O2 concentration affected the decolorization of dyes and the catalyst maintained excellent reusability and stability after reuse over five cycles. The quenching experiments found that •OH, •O2− and h+ were the main active substances and reaction mechanisms were further proposed. The study suggests that the synergistic effect of photocatalysis and Fenton oxidation process significantly improved the removal of azo dyes and the synthesized catalyst had potentially promising applications for difficult-to-biodegrade organic pollutants in wastewater.