Total phenols were determined by high performance liquid chromatography(HPLC) and the metabolomics were analyzed by LC-MS technique for the experimental material, Magnolia officinalis The studied sample did exposed root and embedded trunk treatments with the root bark and trunk bark as the control. The results showed that the total phenolic content of trunk bark and root bark increased in both the embedded trunk and exposed root treatments. 107 of 873 detected metabolites in Magnolia officinalis, were significantly different between the control root bark and control trunk bark group; 71 metabolites were significantly different between the exposed root bark and control trunk bark group, and 76 metabolites were significantly different between the embedded trunk bark and control root bark group. These differential metabolites among the treatment groups were mainly up-regulated. The simulated treatment of root trunk reverse growth caused significant differences in lipids and lipid compounds, organic acids and their derivatives, organic oxides, lignans, neolignans and their related compounds; and the differential metabolites were mainly clustered in β-alanine metabolism, histidine metabolism and other pathways. The root trunk reverse growth simulation treatment induced a significant decrease in the amount of differential metabolites between the treated and simulated sites, and caused a positive response of amino acids and metabolic pathways.