Fluid-structure interaction (FSI) problems in microchannels play prominent roles in many engineering applications. The present study is an effort towards the simulation of flow in microchannel considering FSI. Top boundary of the microchannel is assumed to be rigid and the bottom boundary, which is modeled as a Bernoulli-Euler beam, is simulated by size-dependent beam elements for finite element method (FEM) based on a modified couple stress theory. The lattice Boltzmann method (LBM) using D2Q13 LB model is coupled to the FEM in order to solve fluid part of FSI problem. In the present study, the governing equations are non-dimensionalized and the set of dimensionless groups is exhibited to show their effects on micro-beam displacement. The numerical results show that the displacements of the micro-beam predicted by the size-dependent beam element are smaller than those by the classical beam element.