Analysis of developmental genetic effects for brown rice thickness (BRT) trait in indica rice (Oryza sativa L.) at four different filling stages was conducted and a developmental genetic model and corresponding statistical approaches for quantitative traits of triploid endosperm in cereal crops was used. The results indicated that the diploid maternal plant, triploid endosperm and cytoplasmic genetic effects were important for BRT trait at all filling stages of rice and those effects were the major effect at initial medium, filling period and mature period respectively. The additive and dominance effects were the major effect alternatively at four filling stages of rice. Significant endosperm and maternal dominance effects for BRT suggest that the utilization of heterosis for BRT is viable. The results of conditional genetic variance components shown that the expression of new quantitative genes in endosperm, cytoplasm and maternal plant for BRT was found at most filling stages of rice. The gene expression was most active at the early filling stages, especially at the second stage (8-14 days after flowering). Near to mature period (22-28 days after flowering), however, the expression of genes decreased sharply and even closed. The phenomena that the genes expressed spasmodically, i.e. the net genetic effects equaled to zero in some filling stages were detected for some genetic effects. Dominance and cytoplasmic correlation coefficients were significant at 0.05 or 0.01 probability level in some filling stages meanwhile there were the most strong relationship between mature period and other periods for BRT.