Diatom frustules with hierarchical structures have been widely investigated in many fields due to their unique optical features, excellent mechanical resistance and extraordinarily intricate pore patterns. Herein, Cu2-xS modified diatomite has been successfully fabricated for the first time via a mild method at room temperature. The Cu2-xS nanoparticles with diameters of 50-100 nm were uniformly distributed on the diatomite. The as-prepared Cu2-xS-diatomite (Cu2-xS-DE) exhibits excellent photocatalytic degradation efficiencies for MB and MO, which reach to 99.1% and 96.9% respectively in 40 min under the irradiation of UV-vis light with 20 mg photocatalyst. The degradation mechanism of the organic pollutant over the Cu2-xS-DE/H2O2 reaction system was also proposed. This work provides an effective strategy to design and prepare of the diatom-based nanomaterials with efficient photocatalytic degradation activity, which is of great value for the environmental applications.