The aim of the present study was to find some important metabolic biomarkers of Arabidopsis thaliana roots infected with Plasmodiophora brassicae at the late infection stage. P. brassicae spores were extracted from callus cultures of clubroot gall sections, cocultured with A. thaliana seeds on 1/2 MS medium and then after 45 d metabolic changes of the A. thaliana roots were analyzed by liquid chromatographymass spectrometry (LC-MS) technique. The results showed that P. brassicae could grow and develop in callus, and after cocultured with A. thaliana for 45 d, microscopic observation showed that the pathogens had a complete life cycle on the medium. Multivariate statistical methods of PCA and PLSDA suggested that the metabolities of experimental group (inoculated with P. brassicae) and control group (uninoculated with P. brassicae) differentially expressed. The results of OPLS-DA and t-test showed that the metabolites of flavonoids, lignans, terpenoids, steroidal glycosides, brassinosteroids and phospholipids were significantly increased during P. brassicae infection, suggesting their potential important roles in interaction between A. thaliana and P. brassicae at the late stage of infection.