Background: Co-occurrence of cold and drought stress can alter the response of plants at morphological, physiological and molecular levels, which finally affect crop production, more than individual stress. Understanding the responses of crop to combined stress is necessary to improve tolerance and maintain crop production especially in the field where combined stress frequently occurs. We aimed to clarify the underlying leaf physiological and molecular mechanisms of tomato by imposing combining cold and drought on one popular tomato cultivar 'Jinlingmeiyu' as an example. Results: The physiological and genetic responses were identified in tomatoes after 42 h exposure to control, cold, drought and combined treatments. As compared with control, water loss rate at the three stresses including cold, drought and combined stress significantly decreased until 40 min after taking samples from the plants. The content of H₂O₂, zeatin riboside (ZR) and melatonin in all stress treatments were significantly higher than the control. Drought stress alone and combined stress induced the accumulation of abscisic acid (ABA) and auxin (IAA) as compared with control. The individual cold and combined stress significantly decreased the maximum quantum efficiency of PSII (F_v/F_m), quantum yield of PSII (F_q ^′/F_m ^′) and electron transport rate (ETR). In total, 7141, 1850 and 7841 genes were involved in the stress response to cold, drought and their combination. Functional analysis of the stress-inducible genes provided more insights concerning the complex regulatory mechanisms that were involved in combined stress. The expression level of 12 genes were validated by quantitative real-time PCR (qRT-PCR). Conclusions: We found that the expression of stress-specific genes changed with physiological variation, indicating the close crosstalk between physiological and genetic response especially under combined stress. This study provides new knowledge on the complex regulatory mechanism genes in tomato ('Jinlingmeiyu') leaf to abiotic stresses.