Chinese dwarf cherry (Cerasus humilis), which is well known as “calcium fruit” for its high calcium content, is widely utilized in North China for its ecological and economical value. Understanding the evolutionary history and genetic basis underlying the calcium accumulation in this fruit is a fundamental goal in comparative genomics. In this study, we obtained a chromosome-scale C. humilis genome for the cultivar “zhisha” using PacBio and Proximo Hi-C technologies. The final assembled genome lengths were 235.41 Mb with an N50 contig length of 3.23 Mb. The genome contained 26,800 protein-coding genes, while 41.33% of the genome length consisted of TEs. Phylogenetic analysis revealed that C. humilis displayed a close relationship with Prunus and phylogenetically diverged from its common ancestor ~23.2 million years ago (MYA). Functional enrichment of expanded gene families in C. humilis genome highlighted genes involved in signal transduction, antiporter activity, polygalacturonase activity, auxin efflux transmembrane transporter activity, and auxin efflux, which is related to calcium transport and distribution. Phylogenetic analysis coupled with tissue-specific expression patterns indicated that PSGs identified in this study, such as WAK2 and CBL10, may also be responsible for the high Ca2+ accumulation ability in C. humilis. These results glean tremendous insight into the fundamental genetic basis of the high calcium content in C. humilis fruit. In addition, the reference C. humilis genome we present in this study will be valuable resources for breeding of this fruit species and molecular evolution analysis with related species.