To explore the influence of nonuniform heat transfer on the grain structure and microsegregation of carbon in shells inside the mold, a multiscale model considering heat conduction and dendritic growth is constructed for the round billet continuous casting. Adopting measured heat flux as the boundary conditions, heat conduction in the mold is solved by the finite difference scheme, and dendritic growth is modeled by the cellular automaton model. The temperature distribution of the round billet under measured heat flux is calculated, and the grain structure and the microsegregation of carbon in four selected regions are simulated. Herein, it is shown in the results that the different local heat fluxes lead to dissimilar variations in the surface temperature and grain structure of the shell. A close relationship exists between the carbon microsegregation and local heat flux; the carbon microsegregation decreases with heat flux. The high heat flux accelerates columnar dendritic growth and fines the columnar dendritic array so that the secondary arms are less developed and the microsegregation is improved.