To study the effects of maternal and endosperm quantitative trait locus (QTL) interaction on endosperm development, we derive a two-stage hierarchical statistical model within the maximum-likelihood context, implemented with an expectation-maximization algorithm. A model incorporating both maternal and offspring marker information can improve the accuracy and precision of genetic mapping. Extensive simulations under different sampling strategies, heritability levels and gene action modes were performed to investigate the statistical properties of the model. The QTL location and parameters are better estimated when two QTLs are located at different intervals than when they are located at the same interval. Also, the additive effect of the offspring QTLs is better estimated than the additive effect of the maternal QTLs. The implications of our model for agricultural and evolutionary genetic research are discussed.