Molecular detection was performed by SSR technique for 10 rice variant lines treated by embryo-soaking of Alternanthera philoxeroides DNA solution. The result showed that partial DNA segments of Alternanthera philoxeroides have been transferred into 10 rice variant lines. Based on the molecular evidence, Drought resistance evaluation were further studied using 8 rice variant lines and 2 control varieties in the study, designed by split-plot and analyzed by many statistic methods such as principal component analysis and regression analysis step by step. The results showed that combination the comprehensive evaluation index with drought resistance index could improve the reliability of evaluation for drought tolerance in rice. Cluster analysis based on the two indexes indicated that variant line H8 was the most drought-resistant and H6 and H7 were more drought-resistant than IAPAR9. These results will be important for breeding drought-resistant rice varieties and evaluating drought resistance.