The heat transfer characteristics of the thermally developing flow in the circular and parallel plates microchannels under the constant wall temperature and the constant heat flux are studied analytically. The energy equations are solved by using the separation of variables combined with the Gram–Schmidt orthogonalization. The effect of the number of eigenvalues on the calculation accuracy of the local Nusselt number is first determined. The temperature distribution and the heat transfer coefficient at the entrance region arecalculated considering the effects of the rarefaction (0<Kn<0.1) and the axial heat conduction (Pe>50). It is found that the axial heat conduction can dramatically improve the heat transfer of the thermally developing flow when the Peclet number is less than 250. But when the Peclet number is greater than 500, the effect of the axial heat conduction can be omitted. Enhancing the rarefaction would weaken the influence of the axial heat conduction on the heat transfer, and the difference of the local Nusselt number between the two boundaryconditions decreases as increasing Kn. Enhancing fluid axial heat conduction would increase the thermal entrance length. The thermal entrance length of the microtube is 3–4 times that of the parallel plates microchannel, and the correlations of the thermal entrance lengths are developed, which may provide guidance for thermal design and optimization of microchannel heat sinks.