The medicinal materials of Cistanche tubulosa (CW) and Cistanche deserticola (CD) were selected to carry out the determination of bioactive substances and antioxidant activity and multivariate statistical analysis. The results of active substance analysis showed that there were significant differences in the content of total polysaccharides between the two varieties, and there were significant differences in the contents of total polyphenols, total flavonoids, total triterpenoids, proanthocyanidins, phenylethanoid glycosides, amino acids, proteins and heavy metals. The total polysaccharides in CW were higher than those in CD. The contents of total polyphenols, total flavonoids, total triterpenes and phenylethanoid glycosides in CW were significantly higher than those in CD. The contents of amino acids, proteins and heavy metals in CD were higher than those in CW. The results of antioxidant analysis showed that the DPPH free radical scavenging ability, ABTS free radical scavenging ability and ORAC superoxide radical scavenging ability of CW were significantly higher than those of CD, and there was a significant difference between the two varieties. Correlation analysis showed that the antioxidant capacity of Cistanches herba was closely related to the contents of total polyphenols, total flavonoids, total triterpenes, total polysaccharides, phenylethanoid glycosides, proanthocyanidins, amino acids, proteins and heavy metals. The samples were divided into two groups by cluster analysis. Four principal components were extracted by principal component analysis, and the cumulative variance contribution rate was 94.15%.