Recently, when modeling transient problems of conjugate heat transfer, the independent construction of grid models for fluid and solid subdomains is increasingly being used. Such grid models, as a rule, are unmatched and require the development of special grid interfaces that match the heat fluxes at the interface. Currently, the most common sequential approach to modeling problems of conjugate heat transfer requires the iterative matching of boundary conditions, which can significantly slow down the process of the convergence of the solution in the case of modeling transient problems with fast processes. The present study is devoted to the development of a direct method for solving conjugate heat transfer problems on grid models consisting of inconsistent grid fragments on adjacent boundaries in which, in the general case, the number and location of nodes do not coincide. A conservative method for the discretization of the heat transfer equation by the direct method in the region of inconsistent interface boundaries between liquid and solid bodies is proposed. The proposed method for matching heat fluxes at mismatched boundaries is based on the principle of forming matched virtual boundaries, proposed in the GGI (General Grid Interface) method. A description of a numerical scheme is presented, which takes into account the different scales of cells and the sharply different thermophysical properties at the interface between liquid and solid media. An algorithm for constructing a conjugate matrix, the form of matrix coefficients responsible for conjugate heat transfer, and methods for calculating them are described. The operability of the presented method is demonstrated by the example of calculating conjugate heat transfer problems, the grid models of which consist of inconsistent grid fragments. The use of the direct conjugation method makes it possible to effectively solve both stationary and non-stationary problems using inconsistent meshes, without the need to modify them in the conjugation region within a single CFD solver.