Addition of transglutaminase (TG) was used to improve the quality of buckwheat noodles. The effect of TG on the water absorption, cooking loss, texture properties and microstructure of buckwheat noodles was investigated, as well as protein polymerization and the mechanism impacting on the quality of noodles by SDS—PAGE and SE—HPLC. The results indicated that addition of TG significantly (P < 0.05) decreased the water absorption and cooking loss of noodles, increased the hardness and tensile force. When adding 0.01% TG, the lowest cooking loss of buckwheat noodles was obtained. In addition, with the increase of TG, RVA viscosity properties of buckwheat noodle flour increased except for breakdown. Furthermore, an obvious decrease in the intensity of the protein bands with lower molecular weight was observed in SDS—PAGE patterns and the SDS extractable protein decreased, which demonstrated that TG promoted the protein cross-linking in the buckwheat noodles. And a tight and continuous protein network was observed by CLSM, which made the starch granules be well embedded in it and thus impacted the quality of buckwheat noodles.