The reduced titanium oxide (TinO2n‐1, 4 ≤ n ≤ 10) material system has attracted considerable attention due to their unique crystal structure and excellent electrical and chemical properties. Interface science and engineering play a very important role in both the synthesis or usage of such material, not only because the commonly observed multiphase coexistence phenomenon during the preparation process, but also due to the special physical and chemical properties brought by the heterogeneous interfaces. The lack of research on the interface structures as well as their influence on the properties seriously hinders the development of TinO2n‐1. In this work, crystallographic model is employed first to predict the crystallographic features of Ti5O9/Ti4O7 interface in titanium oxide nanosystems. The initial lattice correspondence is determined after fully considering the crystal symmetry and structures of Ti5O9 and Ti4O7. To verify the predicted results, Ti5O9/Ti4O7 nanocomposites are prepared through carbothermal reduction reaction, followed by detailed X‐ray diffraction and transmission electron microscopy characterizations. The observed orientation relationships between Ti5O9 and Ti4O7 are consistent with the predicted results, which confirm the application of crystallographic model in the phase transformation in which chemical reaction involved.