A microfluidic device for generating monodisperse chitosan microparticles and separating the desired particle from smaller particles created as a byproduct of this process was described. The purpose of this study is to separate the satellite droplets from their parent droplets to enhance the size uniformity of the desired microparticles. A double T-junction design was first employed to control the emulsification and the separation, respectively. The results show that the size and gap of the parent droplets are tunable by adjusting the water and oil flow rates. A separation ratio of the satellite droplets of more than 99% was observed. The proposed microfluidic chip is capable of generating relatively uniform micro-droplets with well controllable diameter, and it has the added advantages of being a simple, low cost, and high throughput process. In the future this apparatus can be used to fabricate size-controlled monodisperse microparticles to act as drug carriers for biotechnology and biomedicine applications.