Topological crystalline insulators (TCIs) are insulating materials whose topological property relies on generic crystalline symmetries. Based on first-principles calculations, we study a three-dimensional (3D) crystal constructed by stacking two-dimensional TCI layers. Depending on the interlayer interaction, the layered crystal can realize diverse 3D topological phases characterized by two mirror Chern numbers (MCNs) (μ1,μ2) defined on inequivalent mirror-invariant planes in the Brillouin zone. As an example, we demonstrate that new TCI phases can be realized in layered materials such as a PbSe (001) monolayer/h-BN heterostructure and can be tuned by mechanical strain. Our results shed light on the role of the MCNs on inequivalent mirror-symmetric planes in reciprocal space and open new possibilities for finding new topological materials.