With increasing application of rare earth elements (REEs), the resulting environmental safety has attracted extensive attention. When REEs act on plant leaves, REEs can initiate endocytosis in leaf cells, causing more REEs enter plant cells and then severe damage to plants. But when REEs directly act on plant roots, whether and how REEs affect the endocytosis in root cells remain unknown. Here, we characterized effects of lanthanum [La(III)], a REE with high accumulation in environment, on the endocytosis in root cells of Arabidopsis thaliana, and revealed effect mechanism from the perspective of DNA methylation. We found that La(III) enhanced the endocytosis in root cells and the extent of enhancement depended on the dose and time of La(III) exposure: 160 μM > 80 μM >30 μM (12 h); 80 μM > 30 μM >160 μM (24 h); 24 h  > 12 h. La(III)-enhanced endocytosis in root cells resulted from DNA methylation, which was closely related to the expression level of genes encoding DNA methylases/demethylases: CMT3, DRM2 and DNMT2 for 12 h, MET1, CMT1, CMT2, CMT3, DRM2, DNMT2, ROS1, DME, DML2, DML5a, and DML5b for 24 h. Conversely, enhanced endocytosis also promoted the expression level of genes encoding DNA methylases/demethylases. Our findings provide references for understanding the mechanisms by which REEs impact plants.