Experimental and numerical studies of heat transfer for turbulent flow in noncircular duct with rough wall are few and far between. In this study, numerical analysis has been carried out on heat transfer for a developing turbulent flow in a square duct with a rough wall using Reynolds stress model and turbulent heat flux model. Calculated results are compared with the experimental data available. The present method can predict well the mean flow distribution and temperature distribution distorted by the secondary flow of the second kind. From calculations, the similarity which appeared between the mean flow distribution and temperature distribution is not observed near the smooth wall facing the rough wall, while it is observed from the experiment. Although the local Nusselt number of smooth walls are understimated by the present method, the production terms of the normal stress u23, shear stress u1u3 and turbulent heat flux u3 T' are in good agreement with the experimental data.