Lodging is a major problem in buckwheat (Fagopyrum esculentum Moench) production. In this study, we investigated the relationship between anatomical structure together with lignin metabolism and lodging resistance. The results indicated that the lodging resistance of culm in buckwheat was closely related to the anatomical structure and lignin metabolism of culm. The lodging percentage was negatively correlated with snapping resistance parameter of culm (r = –0.907, P < 0.01), lignin content (r = –0.844, P < 0.01), mechanical tissue thickness (r = –0.881, P < 0.01), culm wall thickness (r = –0.947, P < 0.01), vascular bundle area (r = –0.846, P < 0.01), mechanical tissue layer number (r = –0.806, P < 0.05), and large vascular bundle number (r = –0.709, P < 0.05), but positively correlated with lodging index (r = 0.842, P < 0.01). The lignin content was positively correlated with activities of phenylalanine ammonialyase (r = 0.984, P < 0.01), 4-coumarate: CoA ligase (r = 0.927, P < 0.01), and cinnamyl alcohol dehydrogenase (r = 0.862, P < 0.01). Therefore, lignin content in culm, mechanical tissue layer number, mechanical tissue thickness, culm wall thickness, large vascular bundle number, and vascular bundle area can be used as main indicators to evaluate lodging resistance in buckwheat. Buckwheat cultivars with high resistance to culm snapping and lodging usually have high lignin content, large number of mechanical tissue layer, and large number of vascular bundle, and thick mechanical tissue and culm wall, and large vascular bundle area.