Using a newly developed mapping model with endosperm and maternal main effects and QTL environment interaction effects on quantitative quality traits of seed in cereal crops, the investigation of quantitative trait loci (QTLs) located on triploid endosperm and diploid maternal plant genomes for protein content and lysine content of rice grain under different environments was carried out with two backcross (BC1F1 and BC2F1) populations from a set of 241 recombinant inbred lines derived from an elite hybrid cross of Shanyou 63. The results showed a total of 18 QTLs to be associated with these two quality traits of rice, which were subsequently mapped on chromosomes 2, 3, 5, 6, 7, 10, 11 and 12. Three of these QTLs were also found havingQTL environment interaction effects. Therefore, the genetic main effects from QTLs located on chromosomes in endosperm and maternal plant genomes and their QTL environment interaction effects in different environments were all important for protein and lysine contents in rice. The influence of environmental factors on the expression of some QTLs located in different genetic systems could not be ignored for both nutrient quality traits.