The MADS-box gene family, as a core factor regulating floral organ development, plays a key role in floral organ development. In this study, the MADS-box gene family of Prunus humilis B. was systematically analyzed at the whole genome level by bioinformatics methods such as sequence alignment, hidden Markov model and phylogenetic tree analysis, and the expression patterns of PhMADS-box genes in different floral organs were analyzed by RT-qPCR. A total of 35 PhMADS-box genes were identified. The phylogenetic tree divided it into 13 subfamilies. Gene structure and conserved domain analysis showed that Type I members contained typical MADS domains, and Type II members contained typical MADS domains and K domains. The results of chromosome localization and collinearity analysis showed that they were unevenly distributed on 8 chromosomes, and 5 pairs of genes had collinearity. Evolutionary pressure analysis showed that PhMADS-box genes were subjected to purification selection. The analysis of cis-acting elements showed that PhMADS-box genes contained a variety of cis-acting elements related to hormone response such as abscisic acid, auxin, jasmonic acid and stress response such as antioxidant, low temperature and drought. The expression pattern analysis of different floral organs showed that PhMADS-box genes were specifically expressed in sepals, petals, stamens and pistils. The above results provide a theoretical reference for analyzing the mechanism of floral organ development and guiding genetic improvement and breeding of P. humilis.