Radio frequency (RF) heating as an emerging technology is widely used to improve cereal-based food quality. To further investigate effects of RF treatment on buckwheat quality, structures and physicochemical properties of protein and starch in buckwheat were evaluated under various temperatures (80, 90, and 100 °C) and holding times (0, 5, and 10 min). Results showed that protein-starch complexes were reaggregated with the increases of RF heating temperature and time, as well as the values of R1047/1022, crystallinity, random coil, and α-helix significantly decreased, and the values of β-sheet obviously increased. Moreover, viscosities and rheological properties of buckwheat were reduced by the raised RF treatment intensity. Besides, the RF processing had a mostly positive effect on swelling power at low temperature of 30 °C, but contrary effect at high temperatures of 60 °C and 90 °C. However, changes of water solubility index, emulsifying capacity, and emulsion stability depended on the RF processing intensity. These results of the study suggested that buckwheat quality was affected by multiple RF treatment conditions, which can be tailored to develop a RF process having the potential to improve the function of buckwheat flour.