In recent advancement of regenerative medicine, it is strongly needed to develop devices to support active dynamic actuation of minute living cells. In this study, with the aid of finite element method analysis, simple but effective cantilever-type three-dimensional micro vibration actuator to be used within limited space and environment on inverted phase-contrast microscope system is newly developed to stimulate cultured living iPS cells colony directly to promote their differentiation into objective cells. The developed actuator enables us to excite three-dimensional vibrations in its micro-probe with total amplitude of displacement up to 30 µm in each X, Y and Z direction. In order to estimate effect of the actuator, mouse iPS cells colony is stimulated with 10 µm indenting as well as shearing vibrations with frequencies of 1, 5, 10, 15 Hz. Effects of these dynamic stimulations on the differentiation process of the mouse iPS cells are investigated by measuring the immunostained areas of βIII-tubulin and F-actin of the differentiated neural cells with or without the dynamic stimulation. It is found that there is significant difference in differentiation efficiency of the mouse iPS cells into neurons between the statically cultured cells and the dynamically stimulated ones. Also, it is confirmed that the mode of the dynamic stimulation has a decisive influence to promote the differentiation of mouse iPS cells into neurons.