We have researched to control microbubbles in blood vessel by use of the acoustic radiation force for efficient and lower adverse effects medical treatments. However, behavior of microbubbles under the ultrasound exposure is complicated because of many kinds of parameters. In addition blood vessel network in human body is not simple. From these reasons, it is important to estimate emission condition of ultrasound. Therefore, numerical simulation model of microbubbles in flow is introduced. By concerning flow and ultrasound conditions, we have constructed a three-dimensional simulation to reproduce behavior of microbubbles using finite element method (FEM). As the results, the simulation showed good coincidences to the result of experiments in lower frequency, however, radius change of microbubbles and acoustic force perpendicular to the propagation direction should be considered in higher frequency.