Abstract: 【Objectives】To provide the basis for the breeding program of molecular assistant selection (MAS) and map-based cloning of high nutrition efficiency utilization, the traits of quantitative trait locus (QTLs) on nitrogen, phosphorus and potassium utilization in rice were identified. 【Methods】 A set of 105 near-isogenic lines, BC4F8 population was developed by backcrossing between Lijiangxintuanheigu (the stongly cold-tolerant japonica landrace, grant No.2) as a donor parent and Towada (cold-sensitive japonica cultivar) as a recurrent parent, and was used as materials, and were planted in Baiyi (cold water irrigation), Xundian (natural low temperature condition) and Yuxi (normal growing environment) in Yunnan, respectively. Sixteen traits associated with N, P, K utilization were evaluated under three different ecological environments. The phenotypic data of 105 NILs, genetic map containing 180 microsatellite markers with 1820.6 cM of the genome, and 15.67 cM average distance between the markers were used to analyze QTLs of N, P and K utilization in rice by the statistic software of QTL IciMapping V 3.2. 【Results】 The total 56 QTLs were detected under three different environment, and were confirmed to be distributed on chromosome 1, 2, 3, 4, 5, 6, 7, 9, and 10, respectively. The number of QTL for single trait was varied from 1 to 10, and the single QTL accounted for 8.88%-35.30% of the phenotypic variation. N, P and K utilization efficiency of No.12, 27, and 17 QTLs were respectively detected. Six QTLs, qTNA-1a, qTPA-1, qPHI-1, qPHI-6, qPHI-7b, and qKHI-6 were detected under cold stress and normal condition, and had high stability and explained 10.63%-31.57% of the phenotypic variation. Moreover, QTLs showed the cluster distribution in 13 QTL regions of chromosome 1, 3, 4, 5, 6, 7, and 10, and a single QTL controlled 2-5 traits, and most of these traits co-controlled total P accumulation, P dry matter production, P harvest index, K absorption of 100-kg seeds, and K harvest index. 【Conclusions】 In this study, 56 QTLs related to N, P and K utilization in rice were detected, and the QTLs with high contribution might be useful for rice breeding with high nutrition efficiency utilization for N, P and K by MAS. Additionally, 13 genomic regions of QTLs cluster distribution are important candidate regions for further study.