Semen Armeniacae Amarum is a Chinese medicine. The Chinese Pharmacopoeia stipulates that the dried ripe seeds of these four plants (Prunus armeniaca L. var. ansu Maxim., Prunus sibirica L., Prunus mandshurica (Maxim.) Koehne, and Prunus armeniaca L.) can all be used as Semen Armeniacae Amarum. Amygdalin is widely recognized as a key quality marker for standardizing Semen Armeniacae Amarum. It exhibits notable antitussive and antiasthmatic effects, and is believed to relieve cough by modulating the activity of the respiratory center. Its diverse pharmacological properties position it as a potential lead compound in drug discovery and the development of novel therapeutics. Climate change has a significant impact on distribution of the aforementioned species and the accumulation of their bioactive components. In this study, the distribution site information of all four plant species was collected through field surveys and online data surveys. Using the Internal Transcribed Spacer 2 (ITS2), the attribution of bitter almonds in each species from different geographical region was identified and the amygdalin content was measured. The maximum entropy model was coupled with the stepwise regression algorithm to evaluate the potential impact of future climate on the quality of amygdalin. The results showed that the 26 samples collected from different producing areas were all identified as PS. Under various Representative Concentration Pathway (RCP2.6, RCP4.5, and RCP8.5), the projected future distribution ranges of Prunus sibirica L. (PS) and Prunus armeniaca L. (PA) are predicted to contract, whereas the range of Prunus mandshurica (Maxim.) Koehne (PK) is projected to expand slightly. The distribution range of Prunus armeniaca L. var. ansu Maxim. (PM) is expected to either expand or contract, depending on specific scenarios and timeframes. Specifically, an expansion is projected under RCP2.6 in both the 2050s and 2070s, and under RCP8.5 in the 2050s. Conversely, a contraction is projected under RCP4.5 in the 2050s and 2070s, and under RCP8.5 in the 2070s. From the perspective of secondary metabolism, amygdalin content exhibits a strong positive correlation with temperature and precipitation. These findings provide valuable guidance for optimizing traditional medicine supply chains and formulating targeted conservation strategies for medicinal resources.