Mapping QTL for stem-related traits using RIL population with ultra-high density bin map can better dissect pleiotropic QTL controlling stem architecture that can provide valuable information for maize genetic improvement. The maize stem is one of the most important parts of the plant and is also a component of many agronomic traits in maize. This study aimed to advance our understanding of the genetic mechanisms underlying maize stem traits. A recombinant inbred line (RIL) population derived from a cross between Ye478 and Qi319 was used to identify quantitative trait loci (QTL) controlling stem height (SH), ear height (EH), stem node number (SN), ear node (EN), and stem diameter (SD), and two derived traits (ear height coefficient (EHc) and ear node coefficient (ENc)). Using an available ultra-high density bin map, 46 putative QTL for these traits were detected on chromosomes 1, 3, 4, 5, 6, 7, 8, and 10. Individual QTL explained 3.5-17.7% of the phenotypic variance in different environments. Two QTL for SH, three for EH, two for EHc, one for SN, one for EN, and one for SD were detected in more than one environment. QTL with pleiotropic effects or multiple linked QTL were also identified on chromosomes 1, 3, 4, 6, 8, and 10, which are potential target regions for fine-mapping and marker-assisted selection in maize breeding programs. Further, we discussed segregation of bin markers (mk1630 and mk4452) associated with EHc QTL in the RIL population. We had identified two putative WRKY DNA-binding domain proteins, AC209050.3_FG003 and GRMZM5G851490, and a putative auxin response factor, GRMZM2G437460, which might be involved in regulating plant growth and development, as candidate genes for the control of stem architecture.