The six morphological traits including plant height，leaf length and bulb diameter，leaf width，mid-plant width and root beard length of Allium macrostemon from different habitats in Guizhou were compared to comprehensively evaluate the germplasm resources of Allium macrostemon Bunge with elite traits，high content of amino acid and good flavor quality.The content of 17 free amino acids in its bulbs was determined with HPLC.The taste of amino acids and the principal components were analyzed.The results showed that the six traits including plant height，bulb diameter，leaf length，leaf width，mid-plant width and root beard length of A.macrostemon were significantly different among the 9 populations （P<0.05），with coefficients of variation greater than 10%.The 9 populations were clustered into 2 categories with Euclidean distance clustering analysis.The morphological traits of category Ⅱ were more prominent.The results of principal component analysis showed that the cumulative contribution of the first principal component reached 80.967%.The results of comprehensive evaluation showed that the Qiannan population had the highest overall score.The average content of total free amino acid （TFAA） in each population was 6 078.52 mg/kg，with higher TFAA content in the Qiandongnan （10 365.90 mg/kg） and Guiyang （8 174.55 mg/kg） population.Flavor intensity value TAV>1 indicated that the amino acid contributed to the flavor of the samples.The bitter Arginine （TAV=6.81） was the main factor affecting the flavor of A.macrostemon.The results of principal component analysis showed that the cumulative contribution of the first four principal components reached 90.144%，and the highest overall score was obtained by the Qiannan population.It is indicated that there are regional differences in morphological traits and content of flavoring amino acid in A.macrostemon.The Qiannan population has outstanding morphological traits，excellent flavor quality，and high value of development and utilization.