In this work, we have developed the anharmonic Debye model to study the Debye temperature and thermal disorder in Fe-Cr intermetallic alloys. The analytical expressions of the anharmonic effective potential, the effective force constant, the Debye temperature and corresponding frequency, and the atomic mean-square displacement characterizing the Debye-Waller factor have been derived. We have implemented the numerical calculations for Fe-Cr intermetallic systems with various Cr concentration up to temperature 700 K. Our results show that the Debye temperature of Fe-Cr systems increases gradually with the increasing Cr composition. Reversely, the mean-square displacement curve drops gradually with Cr concentration. These effects can be explained by the weaker coupling force between Fe atoms as compared to the Cr atoms. Furthermore, we also show the important contributions of thermal disorder to mean-square displacement at high temperature due to thermal lattice vibrations.