<p><i>Fagopyrum tataricum</i> is a nutraceutically important pseudocereal, yet its agricultural potential remains underutilized due to low seed yield, a narrow genetic base, and the lack of improved cultivars. This study aimed to enhance seed yield and rutin content per plant through induced mutagenesis using gamma rays and ethyl methanesulfonate (EMS). In the M4 generation, six selected mutant lines exhibited significant improvements in both seed yield per plant and rutin content compared to the control. A strong positive correlation was observed between seed yield and rutin content per plant. Seed yield per plant also showed positive associations with key agronomic traits, including the number of inflorescences and flowers per plant, seeds per inflorescence, 100 seed weight, and seed yield per plant. Furthermore, physiological traits such as nitrate reductase activity, chlorophyll, and carotenoid contents were positively correlated with seed yield per plant, indicating a link between primary metabolism and secondary metabolite accumulation. Correlation analysis further revealed that the strength of associations between rutin and protein, rutin and minerals, protein and seed yield per plant, and seed yield per plant and minerals remained largely consistent with those observed in the control. This suggests that while seed yield per plant and rutin content can be significantly improved through mutation breeding, the simultaneous enhancement of seed yield per plant, rutin, protein, and mineral contents may be limited. These findings confirm the effectiveness of mutation breeding in improving both agronomic performance and key biochemical traits in <i>F. tataricum</i>. The selected mutant lines represent valuable genetic resources for future breeding programs aimed at developing high-yielding, nutritionally enriched cultivars.</p>