We have investigated an active size controlled droplet generation system by using magnetically driven microtool (MMT). With a lateral motion of the MMT in microchannels, the continuous phase can be pinched off by the movement of MMT to obtain size-controlled droplets actively. With this method, particle-enclosed droplet can be produced on demand to fit the size of each enclosed particle, and which is difficult to carry out only by the fluid dynamic force. For the current study, the system has been evaluated in terms of the frequency of the actuation of MMT and the size of the produced droplets, and found out the response time to change the droplet size by MMT actuation is one third of that only by the fluid dynamic force. This system contributes to the effective transportation of cells in microchannel.