Experiments were conducted on rapeseed (Brassica napus L.) using a diallel design with nine parents: Youcai 601, Double 20-4, Huashuang 3, Gaoyou 605, Zhongyou 821, Eyouchangjia, Zhong R-888, Tower and Zheshuang 72. The seed developmental process was divided into five stages, namely initial (days 1–15 after flowering), early (days 16–22 after flowering), middle (days 23–29), late (days 30–36), and maturing (days 37–43) developmental stages. The variation of dynamic genetic effects for leucine and isoleucine contents of rapeseed meal was analysed at five developmental stages, across different environments using the genetic models with time-dependent measures. The results from unconditional and conditional analyses indicated that the expression of diploid embryo, cytoplasmic and diploid maternal plant genes were important for leucine and isoleucine contents at different developmental stages of rapeseed, particularly at the initial and early developmental stages. Among different genetic systems, nutrition quality traits were mainly controlled by the accumulative or net maternal main effects and their GE interaction effects, except at maturity when the net diploid embryo effects were larger. The expression of genes was affected by the environmental conditions on 15, 22, 29 or 36 days after flowering, but was more stable at mature stage. For the isoleucine content the narrow-sense heritabilities on 15, 22, 29, 36, and 43 days after flowering were 43.0, 65.7, 60.1, 65.5 and 78.2%, respectively, while for the leucine content the corresponding narrow-sense heritabilities were relatively smaller. The interaction heritabilities were more important than the general heritabilities at the first three developmental times. The improvement for isoleucine content could be achieved by selection based on the higher narrow-sense heritabilities. Various genetic systems exhibited genetic correlations among the developmental times or leucine and isoleucine contents. A simultaneous improvement of leucine and isoleucine contents seems possible because of the significant positive genetic correlation components from different genetic systems at different developmental times.