Keteleeria davidiana var. calcarea is an endangered tree with considerable economic potential that used as timber wood for furniture and house construction. However, the natural population of K. davidiana var. calcarea is very fragmented, which is the cause for its low genetic diversity. In this study, we report the complete chloroplast genome of K. davidiana var. calcarea using Illumina sequencing. The chloroplast genome size is 117,670 bp in length, harboring a pair of very short inverted repeats (IRs) of 262 bp separated by a large single copy (LSC) sequence of 64,634 bp and a small single copy (SSC) sequence of 53,078 bp. The chloroplast genome K. davidiana var. calcarea contains 113 genes (74 protein genes, 35 tRNA genes, and 4 rRNA genes) and the overall GC content is 38.6%. The maximum likelihood phylogenetic analysis shows that K. davidiana var. calcarea is clustered with K. davidiana in genus Keteleeria. This complete chloroplast genome will help us to understand the evolution of K. davidiana var. calcarea and lays the foundations for future studies in this species conservation.