Zinc is an essential micronutrient for many organisms, and it is known to enhance abiotic stress tolerance in various plant species. However, the effect of zinc on temperature stress and physiological changes in the cyanobacterium Arthrospira platensis are unknown. In this paper, physiological and comparative proteomic experiments were conducted to investigate the ameliorative effects of exogenous zinc on the growth of A. platensis under low-temperature stress. The results show that zinc alleviated the inhibitory role of low temperature on A. platensis growth and increased the level of antenna proteins, pigments, and soluble sugar. When compared to the untreated group, the zinc-treated group maintained a higher abundance of differentially expressed proteins involved in photosynthesis, carbon metabolism, amino acid and nucleotide metabolism and signal transduction. Thus, the results of proteomic analysis could explain the zinc-induced physiological effects that are associated with low-temperature tolerance. Taken together, these results suggest that zinc could activate multiple pathways that enhance A. platensis adaption to low-temperature stress.