A novel directional freezing based three-dimensional (3D) printing technique is applied to fabricate graphene aerogel (GA). Thermal property of the graphene ink is one of the key impacts on the material morphology and process efficiency/reliability. We develop a heat transfer model to predict temperature evolution of the printed materials and then estimate layer waiting time based on it. The proposed technique can not only improve the process efficiency and reliability but also serve as a flexible tool to predict and control the microstructure of the printed graphene aerogels. Both the simulation and experiment results demonstrate the efficiency and effectiveness of the proposed approach.