The present study investigated the effect of nitrogen fertilization (NF) at the levels of 0, 45, and 90 kg•ha −1 combined with selected sulfur complex fertilization (SCF) levels of 0 and 45 kg•ha −1 on the nutritional and technological characteristics of buckwheat flour from five varieties. The results showed that the genotype was a critical factor affecting the chemical composition and physicochemical properties of buckwheat flour. NF significantly increased protein, total starch, and amylose content as well as mineral composition but decreased particle size, color value, and water hydration properties. However, SCF enhanced the ash content and decreased the protein content but had no significant effect on the pasting temperature. In addition, the combination of NF and SCF significantly reduced granule size, water solubility, viscosity, and rheological properties with increasing fertilization levels. This study can guide the cultivation of buckwheat with the desired physicochemical properties and provide information for buckwheat-based products in the food industry.