Stem diameter is an important trait that affects the plant architecture in maize (Zea mays L.). In order to study the genetic mechanism of stem diameter in maize, a recombinant inbred line (RIL) population (241 lines) derived from Zheng58 and D863F was used to determine the stem diameter at two environmental conditions, followed by QTL mapping using the best linear unbiased prediction values (BLUP). A total of 6 QTL for stem diameter were detected on chromosome 3, 6 and 10, each of which contributes to the phenotypic variance ranging from 4.30 to 10.73%. By transcriptome analysis, 106 (D863F/Zheng58) differentially expressed genes (DEGs) were identified in the physical intervals of the QTL. Forty-nine genes were up-regulated and 57 genes were down-regulated. GO functional enrichment analysis showed that most of the DEGs were enriched in molecular functions, including catalytic activity, transferase activity, malate dehydrogenase activity, ion binding and so on. KEGG enrichment analysis showed that the DEGs were mainly concentrated in biosynthesis of secondary metabolites, alanine, aspartate and glutamate metabolism, and phenylpropanoid biosynthesis. Twelve candidate genes were identified by integrating analysis of QTL mapping and RNA sequencing. These results enabled future fine mapping and functional analysis of these QTL and their candidate genes, which might provide a reference in marker-assisted maize breeding for ideal architecture.