To investigate compositional characteristics of Helianthus tuberosus from different origins and to establish a scientific quality evaluation system, samples from 41 origins were collected and analyzed for 14 fundamental quality indicators. Compositional differences among origins and the influence of meteorological factors were examined using fingerprint similarity analysis of major sugar components, correlation analysis, and cluster analysis. A comprehensive quality evaluation model for H. tuberosus was constructed by integrating correlation analysis, principal component analysis (PCA), the entropy weight method, and grey relational analysis. The results revealed significant differences in physicochemical component contents of H. tuberosus from different origins (P<0.05), among which total flavonoids exhibited the highest coefficient of variation (63.78%). Fingerprint analysis of major sugar components identified 11 common peaks, with overall similarity values ranging from 0.890 to 0.999, indicating consistent component types but notable differences in their contents. The contents of individual sugars were closely associated with meteorological factors such as rainfall, temperature, and sunshine duration. Cluster analysis classified H. tuberosus samples from the 41 origins into four distinct groups. Correlation analysis and PCA identified four key quality indicators, sucrose pentasaccharide, water content, fructose, and ash, as the core contributors to quality differentiation. Grey relational analysis ranked samples from Baishan (Jilin), Dingxi (Gansu), and Jinzhou (Liaoning) as having the highest comprehensive quality. These findings provide a theoretical basis for the quality evaluation, origin differentiation, and comprehensive utilization of H. tuberosus.