On the basis of micro-scales flow field detected by Micro-PIV experiment, Fluent numerical analytic computing software was utilized to design the optimum micro-scales flow simulating plan. In accordance with features of micro-scales, the micro-scales effect manipulating approaches setting wall roughness element and the porous medium simulating wall roughness element was adopted during the design. In the experiment, using realizable k-ε model and standard k-ω model provided by Fluent software, the relative numerical simulations on the rectangle cross section micro-scales water flowing with side length of 600μm in the case of Re=100 and Re=300 was done. With the comparison of velocity field computed from various numerical analyses and the fitting degree of Micro-PIV experimental outcome, the optimum plan that designing case via the porous medium simulating wall roughness element under the solution of realizable k-εwas acquired.