With discretized particle velocity space, a multi-scale unified gas-kinetic scheme for entire Knudsen number flows has been constructed based on the kinetic model in one-dimensional case [J. Comput. Phys., vol. 229 (2010), pp. 7747-7764]. For the kinetic equation, to extend a one-dimensional scheme to multidimensional flow is not so straightforward. The major factor is that addition of one dimension in physical space causes the distribution function to become two-dimensional, rather than axially symmetric, in velocity space. In this paper, a unified gas-kinetic scheme based on the Shakhov model in two-dimensional space will be presented. Instead of particle-based modeling for the rarefied flow, such as the direct simulation Monte Carlo (DSMC) method, the philosophical principal underlying the current study is a partial-differential-equation (PDE)-based modeling. Since the valid scale of the kinetic equation and the scale of mesh size and time step may be significantly different, the gas evolution in a discretized space is modeled with the help of kinetic equation, instead of directly solving the partial differential equation. Due to the use of both hydrodynamic and kinetic scales flow physics in a gas evolution model at the cell interface, the unified scheme can basically present accurate solution in all flow regimes from the free molecule to the Navier-Stokes solutions. In comparison with the DSMC and Navier-Stokes flow solvers, the current method is much more efficient than DSMC in low speed transition and continuum flow regimes, and it has better capability than NS solver in capturing of non-equilibrium flow physics in the transition and rarefied flow regimes. As a result, the current method can be useful in the flow simulation where both continuum and rarefied flow physics needs to be resolved in a single computation. This paper will extensively evaluate the performance of the unified scheme from free molecule to continuum NS solutions, and from low speed micro-flow to high speed non-equilibrium aerodynamics. The test cases clearly demonstrate that the unified scheme is a reliable method for the rarefied flow computations, and the scheme provides an important tool in the study of non-equilibrium flow.