Lotus roots are widely consumed vegetables because of their great taste and abundant nutrients, but their quality varies with the environments and cultivar. This study systematically compared farinose (Elian No. 5) and crisp (Elian No. 6) lotus root cultivars from three geographical origins. Pasting and texture characteristics verified that Elian No. 5 possessed lower hardness and lower ability to withstand shear stress and heating during cooking compared with Elian No. 6. Untargeted metabolite profiling was first performed using ultrahigh-performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) combined with a Zeno trap. In total, 188 metabolites were identified based on the matching chemistry database. Multivariate analysis demonstrated that lotus roots from different cultivars and origins could be adequately distinguished. Sixty-one differential metabolites were identified among three Elian No. 5 samples, and 28 were identified among three Elian No. 6 samples. Isoscopoletin, scopoletin, and paprazine were the most differential metabolites between Elian No. 5 and Elian No. 6. These results can inform future research on the discrimination and utilization of lotus roots.