This paper presents a two-scale topology optimization framework for determining the optimal microstructure in porous material under transient heat conduction and transfer. The new optimization model, which can consider the surface area directly from microstructure topology as the size-dependent term, is introduced to enhance the heat transfer performance. In more detail, a homogenization method capable of considering the size-dependent microscopic heat transfer effect is adopted to express the microscopic material responses. A well-known material interpolation, referred to as the SIMP approach, and the design-dependent linear function are used for interpolating intermediate material properties. The minimal transient heat compliance is chosen as an objective function in this optimization problem. For the sensitivity analysis, a coupled-adjoint variable method is adopted to derive transient sensitivity formulation. The analysis shows that the proposed topology optimization model captures not only the transient heat but also the size effect of the microstructure in a transient heat analysis in porous material.