While the individual influences of melatonin (MT) and polyamines (PAs) have been widely studied under various abiotic stresses, little is known about their interaction under salinity stress. In the present study, salt stress applied by 50 mM of sodium chloride (NaCl) on snap bean seedlings has been supplemented with 20 μM of MT and/or 100 μM of putrescine (Put) (individually and in combination). The results indicated that under salinity stress, the combination of MT + Put achieved the highest significant increase in shoot fresh and dry weight, chlorophyll (Chl a), Chl a + b, carotenoids, total soluble sugars, proline, K, Ca, and cell membrane stability index (CMSI), as well as catalase (CAT) and peroxidase (POX) activities. This improvement was associated with an obvious decrease in Na, Na/K ratio, and oxidative damage as indicated by reducing leaf contents of methylglyoxal (MG), hydrogen peroxide (H2O2), and the rate of lipid peroxidation (malondialdehyde; MDA). Moreover, the combination of MT + Put demonstrated a significant decrease in the activities of diamine oxidase (DAO) and polyamine oxidase (PAO) leading to the reduction of the rate of polyamine oxidation. Meanwhile, MT applied individually gave the highest significant increase in leaf relative water content (RWC), Chl b, superoxide dismutase (SOD), and ascorbate peroxidase (APX). Conclusively, the combination treatment of MT + Put could decrease the degradation of polyamines and enhance tolerance to salinity stress in snap bean seedlings.