The invention relates to an application of a composition of variable sites selected from an EB virus genome to preparing of an EB virus typing kit, and the EB virus typing kit based on detection of the variable sites, in particular to an application of a composition of five variable sites selected from an EB virus genome to preparing of an EB virus typing kit. The variable sites include loc613, 1oc632, loc7048, loc44531 and 1oc146628. The EB virus typing kit based on detection of the variable sites comprises a PCR amplification primer and a single-base extension primer of the composition of the five variable sites of the EB virus genome, and the variable sites include loc613, 1oc632, loc7048, loc44531 and 1oc146628. According to the EB virus typing kit, an EB virus subtype classification standard can be built, and the relative risk degree for individuals to suffer from nasopharyngeal carcinoma is estimated; the EB virus typing kit is suitable for screening of people in a high nasopharyngeal-carcinoma incidence area, and has the positive guiding significance and the important application value for tumor preventing, tumor early diagnosing and early curing and prognosis improving.