To realize in vivo, real-time, non-invasive and in-situ detection analysis on the dynamic changes of ion flows in plant tissues, organs, cells and others under natural conditions, this paper designed three-dimensional electronic control motion platform of high-accuracy so as to realize the highly-accurate motion control in micron order and enable glass microelectrode to measure the plant tissues, organs and cells in its best state. The apparatus requires the portable design, so this paper chose the ion flow detection device with small size and high accuracy and micro integrative drive control module. Also graphical programming software LabVIEW was utilized to send serial port commands so as to realize the accurate and reciprocating motion of glass microelectrode at different positions and further accurately detect the plant microscopic dynamic ion flow parameter. The test showed that this control software could realize highly-accurate positioning of 0.6371μm/step in three-dimensional space and the software system could operate steadily, which provides strong supports for the plant microscopic ion flow detection.