The genus of Prunus subg. Amygdalus are endangered Tertiary-relict plants that are an essential source of woody plant oil. In order to provide a theoretical basis for better protection and utilization of species in the Prunus subg. Amygdalus. This study collected global distribution information for six species within the Prunus subg. Amygdalus, along with data on 29 environmental and climatic factors. The Maximum Entropy (MaxEnt) model was used to simulate the globally suitable distribution areas for these species within the subgenus. The suitable results showed that the area under the test curve (AUC) values of the simulation results were more than 0.8, indicating that the simulation results have high accuracy. Temperature, precipitation, UV-B, and altitude were critical environmental factors affecting the distribution of each species in Prunus subg. Amygdalus. Currently, the distribution area of six species in this genus, from largest to smallest, is Prunus triloba (Lindl.) Ricker, Prunus tenella Batsch, Prunus amygdalus Batsch, Prunus pedunculata Maxim, Prunus mongolica Maxim and Prunus tangutica (Batal.) Korsh. The simulation results of distribution areas showed that under the ssp2.45 and ssp5.85 scenarios, the potential distribution areas of P. amygdalus, P. tangutica, and P. pedunculata all show a decreasing trend, while the distribution areas of P. mongolica and P. tenella, and P. triloba exhibit an increasing trend. The general distribution of P. amygdalus, P. mongolica, and P. tenella will trend to transfer in a northwest direction. P. tangutica and P. pedunculata were affected by other environmental factors (such as slope, altitude, and soil pH), and the distribution area has a tendency to move northeastward. The P. triloba moved to the southwest. The spatiotemporal distribution patterns of Prunus subg. Amygdalus can be used as a reference for forest management and to formulate species conservation strategies.