To engineer effective and efficient food drying solutions, a comprehensive understanding on the related solid and fluid dynamics in food cellular structures is essential. A three-dimensional (3-D) numerical model has been developed to analyze the morphological changes and related transport phenomena of cells situated in parenchyma tissues of apple and potato during drying. This numerical model has been developed based on a meshfree particle method: Smoothed Particle Hydrodynamics (SPH) coupled with a Discrete Element Method (DEM). The proposed model has got the ability to approximate deformations and cellular shrinkage effectively and efficiently specially compared to conventional grid-based Finite Element Methods (FEM) and Finite Difference Methods (FDM). There are two major components in this model: cell fluid model and cell wall model. The cell fluid model is based on SPH and describes the cell protoplasm as a homogeneous Newtonian liquid. The cell wall model is based on DEM and describes the cell wall as an incompressible Neo-Hookean solid. A series of simulations have been conducted to represent the gradual shrinkage of both the apple and potato cells during drying as a function of moisture content in the tissues. Additionally, the sensitivity of model predictions towards several key cellular physical parameters have been presented.