A non-isothermal phase-field model was employed to simulate the columnar formation during rapid solidification in binary Ni–Cu alloy. Heat flux at different boundaries was applied to investigate the temperature gradient effect on the morphology, concentration and temperature distributions during directional solidifications. With the heat flux input/extraction from boundaries, coupling with latent heat release and initial temperature gradient, temperature distributions are significantly changed, leading to solute diffusion changes during the phase-transition. Thus, irregular columnar structures are formed during the directional solidification, and the concentration distribution in solid columnar arms could also be changed due to the different growing speeds and temperature distributions at the solid–liquid interfaces. Therefore, applying specific heat conditions at the solidifying boundaries could be an efficient way to control the microstructure during solidifications.