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The effect of viscosity and viscosity difference and boundary patterned slip on mixing in a micro mixer hasbeen numerically studied using lattice Boltzmann method (LBM). The slip and no-slip ratio is not constant and variesirregularly, and viscosity is altered by changing the relaxation time in LBE equation. The slip boundary condition issimulated by specular reflection boundary and the no-slip boundary condition is simulated by bounce back boundary.It has been found that it is feasible to optimize the micro mixer design by combining the viscosity effect and boundarypatterned ratio altogether.