Drought is an important factor affecting maize yield. In order to explore the drought resistance mechanism of maize seedlings, this study used IlluminaHiseq 2000 to sequence the transcriptome of B73 maize seedlings under the well watering and drought stress conditions. The filtered data was screened for gene differential expression, and the screened differentially expressed genes were analyzed by GO and KEGG. The results showed that differential genes were mainly enriched in cell wall synthesis and glycosylation pathways under the drought stress, which indicated that these two pathways might be closely related to drought resistance in maize seedlings.