3D numerical simulation for penetrative convection of water with density inversion in a rectangular enclosure was performed by the numerical scheme with the combination of finite volume method and SIMPLE method and the results were compared with experimental ones. The inspection of numerical techniques revealed that it is important to obtain rational result that to solve the liner system for pressure correction factor in SIMPLE method accurately. The comparison between numerical results and experimental ones under the same conditions shows that the discrepancy between them becomes remarkable with increasing of hot wall temperature; it implies that the appearance of the problem not only numerical scheme but also in experimental apparatus. Moreover, the occurrence of hysteresis that depends on initial state was also found in numerical result.