The present invention provides a 3D data analysis apparatus and a 3D data analysis method.A 3D data analysis apparatus including a data storage unit that stores measurement data of microparticles, an input unit that selects three kinds of variables independent of the measurement data, a data processing unit that calculates positions and graphics in a coordinate space with the three kinds of variables being coordinate axes and creates a 3D stereoscopic image that represents a characteristic distribution of the microparticles, and a display unit that displays the 3D stereoscopic image, and the 3D data analysis apparatus variably sets a separate area in the coordinate space on the basis of an input signal from the input unit and displays the area in the 3D stereoscopic image.