The heat transfer of natural convection in three dimensional horizontal parallel plates with a heated bottom surface is investigated numerically. For enlarging the application domain, the compressibility of the fluid is taken into consideration instead of the Boussinesq assumption. Numerical methods of the Roe scheme, preconditioning and dual time stepping are adopted for solving governing equations of a low speed compressible flow. A non-reflection condition is used at both apertures in order to decrease computational grids and a CUDA computational platform is developed to economize massive computing time. Variations of thermal and flow fields are examined in detail. The results show that accompanied with elongating the length of the heated bottom surface, both thermal and flow fields are changed from a steady to an unsteady situation. (C) 2012 Elsevier Ltd. All rights reserved.