Numerical techniques for subsurface flow and transport modeling are often limited by computational limitations including fine mesh and small time steps to control artificial dispersion. Particle-tracking simulation offers a robust alternative for modeling solute transport in subsurface formations. However, the modeling scale usually differs substantially from the rock measurement scale, and the scale-up of measurements have to be made accounting for the pattern of spatial heterogeneity exhibited at different scales. Therefore, it is important to construct accurate coarse-scale simulations that are capable of capturing the uncertainties in reservoir and transport attributes due to scale-up. A statistical scale-up procedure developed in our previous work is extended by considering the effects of unresolved (residual) heterogeneity below the resolution of the finest modeling scale in 3D. First, a scale-up procedure based on the concept of volume variance is employed to construct realizations of permeability and porosity at the (coarse) transport modeling scale, at which flow or transport simulation is performed. Next, to compute various effective transport parameters, a series of realizations exhibiting detailed heterogeneities at the fine scale, whose domain size is the same as the transport modeling scale, are generated. These realizations are subjected to a hybrid particle-tracking simulation. Probabilistic transition time is considered, borrowing the idea from the continuous time random walk (CTRW) technique to account for any sub-scale heterogeneity at the fine scale level. The approach is validated against analytical solutions and general CTRW formulation. Finally, coarse-scale transport variables (i.e., dispersivities and parameterization of transition time distribution) are calibrated by minimizing the mismatch in effluent history with the equivalent averaged models. Construction of conditional probability distributions of effective parameters is facilitated by integrating the results over the entire suite of realizations. The proposed method is flexible, as it does not invoke any explicit assumption regarding the multivariate distribution of the heterogeneity. In contrast to other hierarchical CTRW formulation for modeling multi-scale heterogeneities, the proposed approach does not impose any length scale requirement regarding sub-grid heterogeneities. In fact, it aims to capture the uncertainty in effective reservoir and transport properties due to the presence of heterogeneity at the intermediate scale, which is larger than the finest resolution of heterogeneity but smaller than the representative elementary volume, but it is often comparable to the transport modeling scale.