Tomato is usually affected by various abiotic stresses such as low temperature and drought during its growth and development. WRKY transcription factors are involved in the regulation of different plant abiotic stress responses. However, the function of tomato SlWRKY45 in abiotic stress response remains unknown. The expression analysis showed that low temperature, drought and abscisic acid (ABA) treatments could significantly induced the expression of SlWRKY45. Overexpression of SlWRKY45 improved the resistance of tomato to drought and low temperature stresses. The photosynthetic indices, antioxidase activities and proline (Pro) contents of overexpression lines (SlWRKY45-OE) were significantly higher than those of wild type (WT) under drought and low temperature treatments. While the accumulation of reactive oxygen species (ROS) and malondialdehyde (MDA) contents of SlWRKY45-OE were significantly lower than those of WT under drought and low temperature treatments. The transcriptome data analysis showed that SlWRKY45 regulated tomato response to low temperature stress mainly by affecting antioxidase activities and stress response pathways. The analysis of double luciferase assay showed that SlWRKY45 could directly activate the expression of SlPOD1. Moreover, the interaction between SlWRKY45 and SlWRKY46 was confirmed by yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC). These findings indicate that SlWRKY45 plays important roles in tomato resistance to low temperature and drought stresses, and provide potential gene resource in genetic improvement through molecular breeding.