A microscale heterogeneity quantification methodology is presented, which uses petrographic image analysis with multiscale simulation. Petrographic images of micro-porous carbonate rocks are converted into microscale models with help of an image analysis workflow, which helps in assigning specific porosity, permeability and petro-physical properties to the microscale model. Thin section images are discretized into classes of specific porosity. Each specific porosity class is then assigned a permeability using the Kozeny-Carman equation for permeability. Doing so, the thin section image is transformed into a 2D porosity and permeability grid preserving the true heterogeneity at microscale. A multi-scale flow simulation using mixed finite element formulation is then used to perform fast flow simulation on the reconstructed grid representing the microscale model. Although researcher have used pore-network or Lattice-Boltzmann modeling techniques to understand impact of fine scale heterogeneities on fluid flow in porous media, these methodologies are computationally very expensive and impractical for large scale application. Authors present a pragmatic and time-efficient approach for simulating flow experiments at the microscale providing valuable insights into the impact of petrographic components on flow characteristics. A methodology which uses multi-scale methods flow simulations at microscale level has not been presented before in literature.