In this study, we developed a code which can calculate three-dimensional micro multi-phase flow using Moving Particle Semi-implicit method. Surface tension which dominates the fluid motion in micro flow also makes the time steps very small and the simulation time becomes very long. We employed a sub-time steps algorithm that enable us stable and efficient calculation of micro fluid with strong surface tension. Using developed code, micro droplet generation in y-shaped micro channel is calculated. We could realize micro droplet generation in our calculation as the same as experiment. In our calculated results, we measured droplet size. The measured droplet size quantitatively agrees with experimental ones. We also visualize flow inside of droplet when a droplet is generated in the calculated results.