Three Stachys sieboldii Miq.varieties were used to study the effects of waterlogging stress on the physiological characteristics of S. sieboldii Miq..Correlation analysis and principal component analysis were used to evaluate the waterlogging resistance of S. sieboldii Miq. to provide a reference for the identification of waterlogging resistance of S. sieboldii Miq..The results showed that the content of chlorophyll，soluble sugar，soluble protein，and the activity of POD and CAT of the three S. sieboldii Miq.varieties increased first and then decreased with the prolongation of waterlogging stress.The content of Pro in Luyin No.1 and Ganyin No.1 first increased and then decreased，while the content of Pro in Guizai No.1 kept increasing.The activity of SOD in Guizai NO.1 and Luyin No.1 increased first and then decreased，while the activity of SOD in Ganyin No.1 kept increasing under the waterlogging stress.The accumulation of MDA in the three S. sieboldii Miq. varieties increased all the time with the extension of stress time.The results of correlation analyses showed that the content of chlorophyll，soluble sugar，soluble protein，Pro，and MDA，the activity of SOD，POD，and CAT of S. sieboldii Miq.was closely related，but the degree of correlation was inconsistent.The results of comprehensively evaluating waterlogging resistance based on the principal component analysis showed that the waterlogging resistance of the three S. sieboldii Miq. varieties was in the decreasing order of Ganyin No.1>Luyin No.1> Guizai No.1.