Although plant-specific NAC transcription factors play crucial roles in response to abiotic stress, few reports have described the regulation of ZmNAC genes by the cis-natural antisense transcripts (cis-NATs). In the study, 521 NAC genes from Gramineae were classified, of which 51 NAC genes contained cis-NATs. ZmNAC48 and cis-NATZmNAC48 were co-localized to the same cell nuclei and both transcripts responded to drought stress. Arabidopsis overexpressing ZmNAC48 had improved drought tolerance, with lower rate of water loss, enhanced stomatal closure, and higher rates of plant survival. Transient expression in both maize protoplasts and tobacco leaves indicated that cis-NATZmNAC48 reduced ZmNAC48 expression. Western blotting and ribosome profiling analyses confirmed that cis-NATZmNAC48 lacks protein coding potential. Furthermore, the cis-NAT-derived small-interfering RNAs (nat-siRNAs) generated from the overlapping regions of ZmNAC48 and cis-NATZmNAC48 were detected in maize and transgenic Arabidopsis. Cis-NATZmNAC48 overexpressed maize showed higher water loss rate and dead leaves, increased stomatal opening, and decreased expression of ZmNAC48 and nat-siRNA. Taken together, our study indicates that both ZmNAC48 and cis-NATZmNAC48 are involved in plant drought stress response, and that the double-stranded RNA-dependent mechanism is involved in the interaction between cis-NATZmNAC48 and ZmNAC48. Additionally, cis-NATZmNAC48 may negatively regulate ZmNAC48 to affect stomatal closure of maize.