This paper applies the lattice Boltzmann method (LBM) to a 3D simulation of micro flows in an expansion-contraction microchannel. We investigate the flow field under various inlet flow rates and cavity structures, and then systematically study the flow features of the vortex and Dean flow in this channel. Vortex formation analysis demonstrates that there is no observable vortex generated when the inlet flow rate is low enough. As the inlet flow rate increases, a small vortex first appears near the inlet, and then this vortex region will keep expanding until it fully occupies the cavity. A smaller cavity width may result in a larger vortex but the vortex is less influenced by cavity length. The Dean flow features at the outlet become more apparent with increasing inlet flow rate and more recirculation regions can be observed in the cross-section under over high inlet flow rate. In order to support the simulation results, some experimental processes are conducted successfully. It validates that the applied model can accurately characterize the flow in the microchannel. Results of simulations and experiments in this paper provide insights into the design and operation of microfluidic systems for particle/cell manipulation.