Allium kangdingense D.F. Xie & X.J. He. a new species from western Sichuan Province, China, is described and illustrated herein. Evidence from morphological and phylogenetic analyses suggested that this new species belongs to section Sikkimensia of subgenus Reticulatobulbosa. It is morphologically closer to A. plurifoliatum and A. zhegushanense but differentiated by its fibrous roots in fuchsia, semiterete and semi-fistulose leaves, cross-section of scape, tepal color, and the base of stamen filaments. Taxonomic delineation and phylogenetic analysis based on nuclear ribosomal internal transcribed spacers (ITS) and four cpDNA (atpI–atpH, trnV–ndhC, rpoB–trnC, trnL–trnF) regions further revealed that Allium kangdingense is related to other species of sect. Sikkimensia, such as A. beesianum, A. sikkimense, A. yuanum, and A. cyaneum. The detailed differences in morphological characters and habitat are presented.