Flag leaf-related traits (FLRTs) are determinant traits affecting plant architecture and yield potential in wheat (Triticum aestivum L.). In this study, a recombinant inbred line population with 188 lines, derived from the cross between Kenong9204 and Jing411, was developed to identify quantitative trait loci (QTL) for flag leaf width (FLW), length (FLL), and area (FLA) under both low nitrogen and high nitrogen treatments. A total of 38 QTLs were detected in eight environments (year x location 9 treatment). Of these, two QTLs for FLW on chromosomes 4B and 6B (qFlw-4B.3 and qFlw-6B.2) and one for FLA on chromosome 5B (qFla-5B) were major stable QTLs. Both phenotypic and QTL mapping analyses indicated that FLW was the major contributor to flag leaf size. To investigate the genetic relationship between FLRTs and yield-related traits (YRTs) at the QTL level, both unconditional and multivariable conditional QTL mapping for YRTs with respect to FLRTs were conducted. Twelve QTL clusters simultaneously controlling FLRTs and YRTs were identified. In comparison with unconditional QTL mapping, conditional QTL mapping analysis revealed that most but not all the QTL for YRTs were improved by FLRTs. At the QTL level, FLA had the greatest contribution to YRTs, followed by FLW and FLL. This study provided a genetic foundation from which to obtain desirable plant architecture and improve yield potential in wheat breeding programs.