Spring maize is usually subjected to low-temperature stress during seed germination, which retards seedling growth even if under a suitable temperature. However, the mechanism underlying maize seed germination under low-temperature stress modulating seedling growth after being transferred to normal temperature is still ambiguous. In this study, we used two maize inbred lines with different low-temperature resistance (SM and RM) to investigate the mechanism. The results showed that the SM line had higher lipid peroxidation and lower total antioxidant capacity and germination percentage than the RM line under low-temperature stress, which indicated that the SM line was more vulnerable to low-temperature stress. Further transcriptome analysis revealed that seed germination under low-temperature stress caused down-regulation of photosynthesis related gene ontology (GO) terms in two lines. Moreover, the SM line displayed down-regulation of ribosome and superoxide dismutase (SOD) related genes, whereas genes involved in SOD and vitamin B6 were up-regulated in the RM line. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that photosynthesis and antioxidant metabolism related pathways played important roles in seed germination in response to low-temperature stress, and the photosynthetic system displayed a higher damage degree in the SM line. Both qRT-PCR and physiological characteristics experiments showed similar results with transcriptome data. Taken together, we propose a model for maize seed germination in response to low-temperature stress.