Nuclear factor-Y (NF-Y) transcription factors are important regulators of several essential biological processes, including embryogenesis, drought resistance, meristem maintenance, and photoperiod-dependent flowering in Arabidopsis. However, the regulatory mechanisms of NF-Ys in maize (Zea mays) are not well understood yet. In this study, we identified an NF-Y transcription factor, ZmNF-YA3. Genome-wide analysis showed that ZmNF-YA3 bound to >6000 sites in the maize genome, 2259 of which are associated with genic sequences. ZmNF-YA3 was found to interact with CONSTANS-like (CO-like) and flowering promoting factor1 (FPF1) through yeast two-hybrid and bimolecular fluorescence complementation (BiFC) assays. Quantitative real-time reverse transcription-PCR (qRT-PCR) combined with yeast one-hybrid assay and EMSA suggested that NF-YA3 could promote early flowering by binding to the FLOWERING LOCUS T-like12 (FT-like12) promoter in maize. Morerover, we also showed that ZmNF-YA3 could improve drought and high-temperature tolerance through binding to the promoter regions of bHLH92, FAMA, and the jasmonic acid activator MYC4, respectively. These results contribute to a comprehensive understanding of the molecular mechanisms and regulatory networks of NF-Y transcription factors in regulating maize flowering time and stress response in maize.