Effective mixing gives strong advantageous impact on microfluidic applications since mixing is in general very slow process motivated by molecular diffusion transport only on the micro-scale. In this work, the mixing characteristics are analyzed in a Y-channel micromixer with obstacles. For the through analysis, our laboratory in-house unstructured grid CFD code is validated through solving a concentration transport in a uniform microchannel. The solutions well correspond to both exact solutions and those from MemCFD. Mixing in a Y-channel micromixer with obstacles is numerically investigated by the in-house code to search the optimal radius and layout of obstacles. From the simulations, the mixing efficiency appears to be proportional to the magnitude of the formation of lateral velocity component. It is also shown that the asymmetric layout and radius enlargement of obstacles greatly improves mixing efficiency.