Using the Illumina HiSeq X Ten sequencing platform and bioinformatics analysis methods, the sequence characteristics of the chloroplast genome of Amygdalus tangutica were analyzed in this study. The results showed that the whole chloroplast genome was a tetrad structure with 158 166 bp and G+C content of 36.8%. 131 genes were annotated, including 86 protein coding genes, 8 rRNA genes, and 37 tRNA genes. The protein coding genes encoded a total of 52 711 codons, of which 33 types were preferred codons. There were 33 SSRs and 13 tandem repeats in the chloroplast genome of A. tangutica. No trinucleotide repeats were detected in SSRs. The distribution of SSRs was not evenly, with most located in the IGS and LSC regions between genes. Based on the whole chloroplast genomic sequences, a phylogenetic tree was also constructed and analyzed. It was found that A. tangutica was closely related to Amygdalus triloba and Amygdalus pedunculata in the same subgenus Amygdalus, as well as Prunus tomentosa.