Caragana microphylla is a leguminosae plant and grows mainly in semi-arid areas of northwest China and Mongolia. However, the lack of studies on C. microphylla reference genes limits the accurate understanding of the molecular biology mechanisms in this crop under abiotic stresses. In this study, we selected nine candidate genes from salt-treated C. microphylla transcriptome data and evaluated their stability by using geNorm, NormFinder, BestKeeper, and RefFinder in salt and drought conditions. In addition, the relative expressions of Delta 1-pyrroline-5-carboxylate synthase 2 (P5CS2) and Catalase 2 (CAT2) were examined to confirm the stability of the candidate reference genes. As a results, glyceraldehyde-3-phosphate dehydrogenase C2 (GAPC2) and 26S proteasome regulatory subunit (RPN5) were the most stable in both salt and drought treatments. The relative expression of P5CS2 and CAT2 also showed more stable levels in normalization by GAPC2 and RPN5 than the most unstable gene, Ubiquitin 4 (UBQ4). Therefore, it is believed that these candidate reference genes selected and validated in our study could be used to study the molecular biological study of response to salt and drought stress in C. microphylla.