N-doped TiO2 nanoparticles modified with carbon (denoted N–TiO2/C) were successfully prepared by a facile one-pot hydrothermal treatment in the presence of L-lysine, which acts as a ligand to control the nanocrystal growth and as a source of nitrogen and carbon. As-prepared nanocomposites were characterized by thermogravimetric analysis (TGA), X-ray diffraction (XRD), transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HRTEM), Raman spectroscopy, ultraviolet–visible (UV–vis) diffuse reflectance spectroscopy, X-ray photoelectron spectroscopy (XPS), Fourier transform infrared spectroscopy (FTIR), electron paramagnetic resonance (EPR) spectra, and N2 adsorption–desorption analysis. The photocatalytic activities of the as-prepared photocatalysts were measured by the degradation of methyl orange (MO) under visible light irradiation at λ ≥ 400 nm. The results show that N–TiO2/C nanocomposites increase absorption in the visible light region and exhibit a higher photocatalytic activity than pure TiO2, commercial P25 and previously reported N-doped TiO2 photocatalysts. We have demonstrated that the nitrogen was doped into the lattice and the carbon species were modified on the surface of the photocatalysts. N-doping narrows the band gap and C-modification enhances the visible light harvesting and accelerates the separation of the photo-generated electrons and holes. As a consequence, the photocatalytic activity is significantly improved. The molar ratio of L-lysine/TiCl4 and the pH of the hydrothermal reaction solution are important factors affecting the photocatalytic activity of the N–TiO2/C; the optimum molar ratio of L-lysine/TiCl4 is 8 and the optimum pH is ca. 4, at which the catalyst exhibits the highest reactivity. Our findings demonstrate that the as-obtained N–TiO2/C photocatalyst is a better and more promising candidate than well studied N-doped TiO2 alternatives as visible light photocatalysts for potential applications in environmental purification.