Robust particle manipulation is a challenging but essential technique for single-cell analysis and processing of microfluidic devices. This paper proposes a micro-particle manipulation system with a microfluidic channel network. We built gravity-induced pressure actuators, which can generate high-resolution output pressure with a wide range so that the multiple particles can be delivered from the inlet of the chip. In this paper, we studied how to model the proposed multi-input-single-output system and sources of disturbances, and designed a robust controller using disturbance observer technique. The performance of the proposed system was verified through experiments.