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The heterophase junction is of great importance in photocatalysis and many other applications. The mechanical, optical and electrical properties of metrical are sensitive to the atomic structure of the heterophase junction. To date, the determination of these structures at the atomic level has been of great challenge for both experiment and theory. In this focused review, we introduce the recently developed theoretical methods based on stochastic surface walking method, which in combination with finite strain theory and first principles calculations can be utilized for identifying the homogeneous phase transition pathway and characterizing the atomic structure at the phase junction. The orientation relation and the atomic habit plane obtained from theory provide the key information for constructing the coherent phase junction. We then discuss the application of the method in two example systems in the context of latest experimental findings, namely TiO-B/anatase and anatase/rutile heterophase junction that are of wide application in photocatalysis. Using these examples, the merits and deficiencies of the current theoretical tools are illustrated. New theoretical approaches are called for towards the simulation of the solid-to-solid phase transition in real time and the characterization of heterostructure junction in general. [ABSTRACT FROM AUTHOR]