The chromatographic peak distinction of 13 secondary compounds from two types of rice varieties were investigated by using high-performance liquid chromatography(HPLC). The result of multiple regression analysis was showed that peak 1, peak 2, peak 8 and peak 12 were major secondary compounds to affect the variety resistance to brown planthopper (BPH, Nilaparvata lugens) biotype II, whereas peak 3, peak 4, peak 5, peak 9, peak 11 and peak 12 were major secondary compounds to Bangladesh biotype of BPH. Two regression equations among the area values of the chromatographic peaks and the BPH-resistant level of rice variety to different biotypes were obtained. It was demonstrated that the resistant activity of rice varieties to different BPH biotypes was closely associated with qualitative and quantitative combinations of the secondary compounds. These secondary compounds were suggested to be used as the marks to evaluated and identified the rice variety resistance to different biotypes of BPH.