To obtain new insights into the mechanisms of the positive effects of exogenous melatonin applications to cucumber seedlings during chilling, we investigated its role in regulating photosynthesis, the transcription level of csZat12 and the metabolism of polyamines (PAs) and of abscisic acid (ABA). The negative effects of chilling were clearly alleviated in cucumber seedlings by irrigation with 200 μM melatonin solution. This was evidenced by alleviation of the decline in net photosynthesis rate and also in electrolyte leakage in chilled plants. The reasons for this can be explained as follows. First, melatonin up-regulates CsZat12, an important stress-related gene. Second, melatonin increases the content of putrescine (Put) and spermidine (Spd) and stabilized spermine (Spm) by altering the activity of the PA metabolic enzymes. And, third, ABA is also involved in these effects as melatonin modulated the expression of the key ABA biosynthesis genes (CsNCED1 and CsNCED2) and also the key ABA catabolism genes (CsCYP707A1 and CsCYP707A2). This study provides new evidence suggesting melatonin mitigates chilling stress in cucumber by up-regulating the expression of CsZat12 and by modulating the metabolism of PAs and ABA.