The research conducted at the Shanxi Agricultural University’s Quinoa Experimental Model Base in Jinzhong, Shanxi Province, aimed to assess agronomic traits and their correlation with yield across 32 quinoa varieties. Three distinct yield categories emerged: low (≤1500 kg ha−1), middle (1500–2500 kg−1), and high (>2500 kg ha−1). High-yielding varieties demonstrated notable characteristics, including decreased plant height and increased leaf area per plant at maturity compared to low- and middle-yielding varieties. Moreover, the decline in leaf area per plant and root traits from flowering to maturity was less pronounced in the high-yielding varieties. The high-yielding varieties had a higher hardness of the stem base and middle stem by 12–13.7% and 6.3–11.5% compared to the medium- and low-yield varieties. Furthermore, high-yielding varieties indicated improvements in dry matter accumulation, decreased effective branch number, and increased main ear length and 1000-grain weight. Correlation analysis highlighted significant relationships between grain weight, yield, post-flowering senescence, and root and leaf characteristics. Structural equation model analysis revealed the negative impact of certain root and leaf traits on grain weight and yield, suggesting their importance in determining productivity. Notably, high-yielding varieties exhibited traits conducive to increased grain weight, including shorter plant height, slower root senescence, and enhanced post-flowering leaf resilience. These findings showed that understanding the relationship between agronomic traits and yield potential is crucial for optimizing quinoa production and promoting the sustainable development of this essential crop.