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Drought is a major abiotic stress factor limiting maize production, and elucidating the genetic control of root system architecture and plasticity to water-deficit stress is a crucial problem to improve drought adaptability. In this study, 13 root and shoot traits and genetic plasticity were evaluated in a recombinant inbred line (RIL) population under well-watered (WW) and water stress (WS) conditions. Significant phenotypic variation was observed for all observed traits both under WW and WS conditions. Most of the measured traits showed significant genotype–environment interaction (GEI) in both environments. Strong correlations were observed among traits in the same class. Multi-environment (ME) and multi-trait (MT) QTL analyses were conducted for all observed traits. A total of 48 QTLs were identified by ME, including 15 QTLs associated with 9 traits showing significant QTL-by-Environment interactions (QEI). QTLs associated with crown root angle (CRA2) and crown root length (CRL1) were identified as having antagonistic pleiotropic effects, while 13 other QTLs showed signs of conditional neutrality (CN), including 9 and 4 QTLs detected under WW and WS conditions, respectively. MT analysis identified 14 pleiotropic QTLs for 13 traits, SNP20 ([email protected] cM) was associated with the length of crown root (CR), primary root (PR), and seminal root (SR) and might contribute to increases in root length under WS condition. Taken together, these findings contribute to our understanding of the phenotypic and genotypic patterns of root plasticity in response to water deficiency, which will be useful to improve drought tolerance in maize.