We present a new model of the three-dimensional distribution of molecular gas in the Milky Way Galaxy, based on CO line data. Our analysis is based on a gas-flow simulation of the inner Galaxy using smoothed-particle hydrodynamics (SPH) using a realistic barred gravitional potential derived from the observed COBE/DIRBE near-IR light distribution. The gas model prescribes the gas orbits much better than a simple circular rotation model and is highly constrained by observations, but it cannot predict local details. In this study, we provide a 3D map of the observed molecular gas distribution using the velocity field from the SPH model. A comparison with studies of the Galactic Center region suggests that the main structures are reproduced but somewhat stretched along the line-of-sight, probably on account of limited resolution of the underlying SPH simulation. The gas model will be publicly available and may prove useful in a number of applications, among them the analysis of diffuse gamma-ray emission as measured with GLAST.