Alfalfa is an important perennial forage but suffers from salt and osmotic stresses worldwide. Calcineurin B-like proteins (CBLs) and CBL-interacting protein kinases (CIPKs) are reported to play important roles in response to diverse plant stresses, but are largely unvalidated in alfalfa. In this study, we cloned a MsCIPK gene, which contained 1530 bp, coding 509 amino acids, with typical CIPK functional domains. The expression pattern of MsCIPK was measured using qRT-PCR under salt, drought, heat, cold and ABA stresses. Under NaCl, heat and ABA treatment, the expression pattern of MsCIPK was generally similar, with a first steady decrease and then a gradual increase pattern. The highest expression of MsCIPK was all observed at the start point of all treatments, except in cold treatment. Using transgenic tobaccos of MsCIPK, we further measured the content of malondialdehyde (MDA), superoxide dismutase (SOD), soluble protein (SOP), and proline (Pro) under 21 days’ salt and 24 hours’ cold treatment. Under both salt and cold conditions, the content of MDA, SOP and Pro had a similar overall increase pattern with the time of treatment. These results indicated that the MsCIPK played an important role in improving alfalfa’s salt and osmotic tolerance.