Objective To study if quantum dots fluorescent probes can be applied to detect P53 protein and Bcl- 2 protein in tissue of human tongue squamous cell carcinoma. Methods By indirect immunofluorescence assay the same particle size quantum dots fluorescent probes were applied to detect P53 protein and Bcl-2 protein respectively. Different particle size quantum dots fluorescent probes were applied to detect P53 protein and Bcl-2 protein simultaneously in paraffin-embedded tissue section of human tongue squamous cell carcinoma under fluorescent microscope. Results P53 protein and Bcl-2 protein can be combined with quantum dots fluorescent probes and specific fluorescene can be observed with ultraviolet light excited. P53 protein was mainly distributed in the nucleus, and Bcl-2 protein major in the cytoplasm. P53 protein and Bcl-2 protein can be combined with different particle size quantum dots fluorescent probes respectively in the same paraffin-embedded tissue section of human tongue squamous cell carcinoma and two kinds of fluorescene can be observed. Conclusion Quantum dots fluorescent probes can be applied to detect two kinds of specific protein in paraffin-embedded tissue section of human tongue squamous cell carcinoma.