This study simulated the natural convection of dissolved carbon dioxide (CO2) in a small-scale heterogeneous saline formation using the state module ECO2N equation in the TOUGHREACT model. A one-way downscaling approach that involves using a series of sub-models in simulation procedures was proposed to efficiently simulate problems with high-scale discrepancies. This study evaluated the effects of different degrees of small-scale permeability variations on the vertical migration of dissolved CO2. The sequential Gaussian simulation model was used to generate unconditional random permeability fields for different natural logarithm of permeability (lnk) variations (i.e., lnk variances and correlations in x and z directions). The results showed an identical transition zone of dissolved CO2 near the top boundary, where a constant CO2 gas saturation was specified. The local permeability variations can trigger fingerings and enhance the vertical convection of the dissolved CO2. The number of fingerings depends on the variations in permeability near the front interface of the dissolved CO2 (i.e., the bottom edge of the transition zone for the dissolved CO2). However, the fingering patterns and developments are constrained by the permeability variations along the fingering paths. At the same mean lnk permeability the convection fluxes increase with an increase in lnk variances. However, an increase in lateral correlations (i.e., increase in the correlation lengths in the x direction) can slightly reduce the convection fluxes at the same lnk variance. The highly variable flux rates of the dissolved CO2 occur early and the variations in the flux rate decrease with time.