Heat flow in heterogeneous media with complex microstructure follows tortuous path and therefore determination of temperature distribution in them is a challenging task. Two-scales, micro-macro model of heat conduction with phase change in such media was considered in the paper. A relation between temperature distribution on the microscopic level, i.e., on the level of details of microstructure, and the temperature distribution on the macroscopic level, i.e., on the level where the properties were homogenized and treated as effective, was derived. The expansion applied to this relation allowed to obtain its more simplified, approximate form corresponding to separation of micro- and macro-scales. Then the validity of this model was checked by performing calculations for 2D microstructure of a composite made of two constituents. The range of application of the proposed micro-macro model was considered in transient states of heat conduction both for the case when the phase change in the material is present and when it is absent. Variation of the effective thermal conductivity with time was considered and a criterion was found for which application of the considered model is justified.