Due to the deformation ability even under small loads, hydrogels have been widely used as a type of soft materials in various applications such as actuating and sensing, and have attracted many researchers to study their behaviors. In this paper, the behavior of hydrogel micro-valves with reverse sensitivity to the pH inside a T-junction flow sorter is investigated. With the fluid-structure interaction (FSI) approach, the effects of various parameters such as the inlet pressure and the pH value on the stress and deformation of the micro-valves are examined, and the results with and without FSI, including the flow rate and the closure pH, are compared. In order to reduce the response time of hydrogels, the effects of three different patterns on the performance of the micro-valves are explored. Eventually, it is concluded that FSI is a key influential factor in designing and analyzing the behaviors of hydrogels.