Abstract: Dielectrophoresis field flow fraction (DEP-FFF) is an efficient method for the separation of micro particles, in which the particles in micro channels are polarized and controlled to separate via a non-uniform electric field. The separation of flexible particles in DEP-FFF are influenced by many complex factors including multiphysics effects, multiphase flows and particle deformation. It is difficult to simulate the process with a single calculation method. In this paper, a finite element-lattice Boltzmann coupling method is introduced to solve this problem. The lattice Boltzmann is a mesoscopic method, in which the micro volumes of a fluid are represented with small particles. The Boltzmann transport equation for fluid dynamics is solved on discrete lattice, such that the multiphase flows and large deformation problems can be easily handled. Due to these advantages, the particle deformation in the DEP-FFF process can be readily handled by the lattice Boltzmann method. On the other hand, the simulation of the total DEP-FFF process requires the solution of the Navier-Stokes equation, dielectrophoresis force equation and particle trajectory equation. The computational burden will be very severe if only the lattice Boltzmann method is employed. By computing the dielectrophoresis force with finite element method, the computational efficiency is significantly improved. The finite element-lattice Boltzmann coupling method is applied in the simulation of the particle separation process within a typical DEP-FFF chip. Analyzing the dielectrophoresis force on the particles produced by the non-uniform electric field, the relationship between the dielectrophoresis force and the change rate of electric field is revealed. The trajectories of the particles under different electric conditions are traced to validate the efficiency of the DEP-FFF method. Most importantly, the deformations of the particle under the non-uniform electric filed are analyzed. It is found that the change of the particle trajectory is controlled by the dielectrophoresis force and thus the non-uniform electric field, while the deformation of the particle is mainly related to the shearing effect of the flows. The finite element-lattice Boltzmann multiscale coupling method introduced in this paper provides an effective solution for the calculation of complex micro flows.