The invention discloses a method for screening effective sites of flavonoid substances in golden camellia acting on nasopharyngeal carcinoma. The method comprises the following steps: extracting flavonoid substances in golden camellia for acting on nasopharyngeal carcinoma cell strains such as CNE-1, CNE-2, C666-1 and the like cultured in vitro and taken as models, discovering that flavonoid-like substances in a golden camellia extract can be used for inhibiting nasopharyngeal carcinoma cell proliferation and inducing apoptosis of nasopharyngeal carcinoma cells by applying a laser confocal inverted microscope, a fluorescence labelling mRNA differential display technology, a proteomics method, matrix-assisted time of flight mass spectroscopy and other technologies, also performing location detection on the expression of genes such as bcl-2, notch1 and the like in nasopharyngeal carcinoma, and revealing the effective sites of the flavonoid substances in golden camellia in inhibition of nasopharyngeal carcinoma activity from the change of protein levels. According to the method disclosed by the invention, deep research can also be performed by virtue of differentially-expressed proteins, action mechanisms of the proteins can be clarified, and meanwhile, the proteins can be possibly taken as action target molecules of medicines for clinically treating nasopharyngeal carcinoma.