In this work we develop a new propagation model for the Galactic cosmic rays based on the GALPROP code, including contributions from dark matter annihilation. Its predictions of the Galactic diffuse $\ensuremath{\gamma}$-ray spectra are compatible with the EGRET data in all sky regions. It also gives consistent results about the diffuse $\ensuremath{\gamma}$ ray longitude and latitude distributions. The $\mathrm{B}/\mathrm{C}$, $^{10}\mathrm{Be}/^{9}\mathrm{Be}$, proton, electron and antiproton spectra are in agreement with cosmic ray measurements as well. In this model we have taken a universal proton spectrum throughout the Galaxy without introducing large fluctuation, considering the proton energy loss is negligible. The dark matter annihilation signals are boosted after taking the contributions from subhalos into account. Another interesting feature of this model is that it gives a better description of the diffuse $\ensuremath{\gamma}$ rays when taking the source distribution compatible with supernova remnants data, which is different from previous studies.