We present a new theoretical population synthesis model (the Galaxy Model) to examine and deal with large amounts of data from surveys of the Milky Way and to decipher the present and past structure and history of our own Galaxy.We assume the Galaxy to consist of a superposition of many composite stellar populations belonging to the thin and thick disks, the stellar halo and the bulge, and to be surrounded by a single dark matter halo component. A global model for the Milky Way's gravitational potential is built up self-consistently with the density profiles from the Poisson equation. In turn, these density profiles are used to generate synthetic probability distribution functions (PDFs) for the distribution of stars in colour-magnitude diagrams (CMDs). Finally, the gravitational potential is used to constrain the stellar kinematics by means of the moment method on a (perturbed)-distribution function. Spiral arms perturb the axisymmetric disk distribution functions in the linear response framework of density-wave theory where we present an analytical formula of the so-called 'reduction factor' using Hypergeometric functions.Finally, we consider an analytical non-axisymmetric model of extinction and an algorithm based on the concept of probability distribution function to handle colour magnitude diagrams with a large number of stars. A genetic algorithm is presented to investigate both the photometric and kinematic parameter space.This galaxy model represents the natural framework to reconstruct the structure of the Milky Way from the heterogeneous data set of surveys such as Gaia-ESO, SEGUE, APOGEE2, RAVE and the Gaia mission.