A genetic model for quantitative traits of seeds in diploid plants was applied to estimate the genetic main effects and genotype × environment (GE) interaction effects for protein content (PC) of rapeseed (Brassica napus L.) by using 2 years of experimental data with a diallel mating design of 8 parents. Results showed that PC of rapeseed was simultaneously controlled by genetic effects of embryo, cytoplasm, and maternal plant, of which the maternal genetic effects were most important, followed by embryo and cytoplasmic genetic effects. Therefore, improvement of PC of rapeseed would be more efficient when selection is based on maternal plants than that on single seeds. Since the GE interaction effects accounted for about 60.10% of total genetic effect, they were more important than the genetic main effects, and selection for PC might be influenced by environmental conditions. The total narrow-sense heritability for PC was 64.17%, of which the interaction heritability was larger than the general heritability. Selection for improving PC can therefore be conducted in early generations. Maternal heritability (41.59%) was most important for PC, followed by cytoplasmic heritability (17.62%) and then by embryo heritability (5.25%). Based on prediction of genetic effects, parent Youcai 601 was better than others for increasing PC in rapeseed breeding.