Black TiO2 with doped nitrogen and modified carbon (b-N-TiO2/C) were successfully prepared by sol-gel method in the presence of urea as a source of nitrogen and carbon. The photocatalysts were characterized by field emission scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), Raman, electron paramagnetic resonance (EPR), and UV-vis diffuse reflectance spectra (DRS). The doped nitrogen, introduced defects, and modified carbon played a synergistic role in enhancing photocatalytic activity of b-N-TiO2/C for the degradation of chlorophyll-a in algae cells. The sample, with a proper amount of phase composition and oxygen vacancies, showed the highest efficiency to degrade chlorophyll-a, and the addition of H2O2 promoted this photocatalysis degradation. Based on the trapping experiments and electron spin resonance (ESR) signals, a photocatalytic mechanism of b-N-TiO2/C was proposed. In the photocatalytic degradation of chlorophyll-a, the major reactive species were identified as OH and O2−. This research may provide new insights into the photocatalytic inactivation of algae cells by composite photocatalysts.