Recent studies show that shear-induced drug loading methods in the microfluidic device is an efficient intracellular drug loading approach. In this study, a cellular-scale numerical model based on dissipative Lattice Boltzmann Method and spring connected network is utilized for modeling the drug encapsulation into a compound cell after rapid squeezing through microfluidic channels. The radius of the shear-induced pores is computed via a mathematical correlation derived from the results of coarse-grained molecular dynamics. We assume that the drug loading occurs after squeezing as a result of passive diffusion. To calculate the drug concentration inside the cell, a mathematical correlation is proposed for passive diffusion after squeezing. The numerical algorithm is validated by simulation a compound cell under simple shear flow.