Abstract This paper proposes a novel droplet transportation method for micro total analysis system (μTAS), which we called as an active flow channel matrix, using an electro-conjugate fluid (ECF). The ECF is a kind of functional fluid, which generates a powerful flow when applying a high voltage across the electrodes. A droplet that is placed into the channel may move in any direction according to the channel flow generated by the ECF. Therefore, in order for the multiple droplets from different channels to be merged, they are moved to reach the desired intersection. According to this concept, we developed a prototype of the active flow channel matrix. Then, we measured two droplets’ position and controlled the position of them by using image processing technique. The experimental results demonstrated the possibility of our concept for μTAS.