Eight rice introgression lines carried the DNA fragments from Alternanthera philoxeroides Griseb and two CKs, including the receptor 6527 (CK1) and a rice cultivar of IAPAR9 (CK2) with well drought tolerance were used to analyze the physiological characterization of drought tolerance of rice with a split plot design. Seven physiological parameters, including the activity of superoxide dismutase (SOD), malondialdehyde (MDA) content, conductivity, proline content, and content of chlorophyll a, chlorophyll b and total chlorophyll were assayed with the stepwise lineal regression analysis and the principal component analysis. The results showed that the introgression line H8 possessed a stronger overall drought-tolerant performance than CK1 and CK2. Furthermore, the results also suggested that MDA, proline, chlorophyll and conductivity could be used as informative indicators in the physical characterization of drought tolerance in rice research.