The high input and low use efficiency of nutrient fertilizers require knowledge of the genetic control of crop reaction to nutrient supplements. In this study, 14 morphological and 8 physiological traits of a set of 182 wheat (Triticum aestivum L.) recombinant inbred lines (Xiaoyan 54 × Jing 411) were investigated in six environments to map quantitative trait loci (QTLs). The influence of nitrogen (N) and phosphorus (P) fertilization on QTL expression was studied by unconditional and conditional analysis. A total of 117 and 30 QTLs were detected by unconditional and conditional analysis, respectively, among which 21 were common for both methods. Thirty-four QTL clusters were identified. Eighteen conserved QTLs (15.4 % of the 117 QTLs) between years, but within nutritional treatment were found. The three major QTLs on chromosomes 2D, 4B and 6A were coincident withRht8, Rht-B1b and TaGW2, respectively. The other two important intervals on chromosomes 4B and 7A for yield component traits were newly detected QTLs that warrant further study. By conditional analysis, spikelet number per spike was found to be induced by P fertilization mostly, whereas N fertilization had more effects on the expression of the QTLs for nitrogen concentration and utilization efficiency traits. QTLs that respond to N and P interactions were also detected. The results are helpful for understanding the genetic basis of N utilization efficiency in wheat under different N and P supplement environments and provide evidence for the availability of conditional analysis in dissecting QTLs induced by environmental factors.