japonica rice is mainly distributed in Northeast China and accounts for 44.6% of the total cultivated area of japonica rice in China. The comprehensive using of inter-subspecies heterosis is the main breeding mode of super japonica rice varieties in this region. Improving rice quality at relative high yielding level is the current research focus. Performing crosses between indica and japonica lines allows for the recombination of regulatory genes and genetic backgrounds, leading to complicated genetic rice quality characteristics, which can be used to explore patterns of quality improvement. In the present study, we utilize recombinant inbred lines(RILs) derived from indica-japonica hybridization to analyze the effect factors of rice quality derived from genetic factors, which contain both regulatory genes concerning rice quality and genetic backgrounds’ random introduction frequency coming from indica(Di value), and the improvement strategy was further discussed. The regulatory genes involved in amylase content(Wx) and nitrogen utilization efficiency(NRT1.1B) were the major factors affecting the amylose content(AC) and protein content(PC) in RILs, respectively. Both the Di value and the major grain width gene(GS5) had regulatory effects on milled rice width(MRW) in RILs, and their interaction explained the major variance of MRW in the RILs. With the mediation of MRW and chalkiness degree(C), Di value had a further impact on head rice rate(HR), which was relatively poor when the Di value was over 40%. In Northeast China, the Di value should be lowered by backcrossing or multiple crosses during the breeding of indica-japonica hybridization to maintain the whole better HR and further to emphasize the use of favorable genes in individual selection. japonica rice is mainly distributed in Northeast China and accounts for 44.6% of the total cultivated area of ​​japonica rice in China. The comprehensive using of inter-subspecies heterosis is the main breeding mode of super japonica rice varieties in this region. Improving rice quality at relative high yielding level is the current research focus. Performing crosses between indica and japonica lines allows for the recombination of regulatory genes and genetic backgrounds, leading to complicated genetic rice quality characteristics, which can be used to explore patterns of quality improvement. study, we Taking recombinant genes in rice quality and genetic backgrounds’ random introduction frequency coming from indica (Di value ), and the improvement strategy was further discussed. The regulatory genes involved in amylase content (Wx) and nitrogen utilization efficiency (NRT1.1B) were the major factors affecting the amylose content (AC) and protein content (PC) in RILs, respectively. Both the Di value and the major grain width gene ) had regulatory effects on milled rice width (MRW) in RILs, and their interaction explained the major variance of MRW in the RILs. With the mediation of MRW and chalkiness degree (C), Di value had a further impact on head rice rate ( HR), which was relatively poor when the Di value was over 40%. In Northeast China, the Di value should be lowered by back cross or multiple crosses during the breeding of indica-japonica hybridization to maintain the whole better HR and further to emphasize the use of favorable genes in individual selection.