Sinolimprichtia alpina var. dissecta is a plant variety which is characterized from S. alpina var. alpina in possessing characteristic, highly dissected bracteoles. In the current study, we have sequenced the complete chloroplast genome of S. alpina var. dissecta using the Illumina sequencing platform. The chloroplast genome is 156,719 bp in length, consisting of a LSC region of 95,625 bp, a SSC region of 10,500 bp, and a pair of inverted repeats (IR) regions of 25,297 bp. The GC content was 37.7%. A total of 126 unique genes were identified, including 81 protein-coding genes, 37 tRNA genes and 8 rRNA genes. Phylogenetic analysis based on 28 chloroplast genomes indicates that S. alpina var. dissecta is most closely related to Pterygopleurum neurophyllum.