The deformation behavior of a pH-sensitive hydrogel micro-fluidic valve system is investigated using inhomogeneous gel deformation theory, in which the fluid-structure interaction (FSI) of the gel solid and fluid flow in the pipe is considered. We use a finite element method with a well adopted hydrogel constitutive equation, which is coded in commercial software, ABAQUS, to simulate the hydrogel valve swelling deformation, while FLUENT is adopted to model the fluid flow in the pipe of the hydrogel valve system. The study demonstrates that FSI significantly affects the gel swelling deformed shapes, fluid flow pressure and velocity patterns. FSI has to be considered in the study on fluid flow regulated by hydrogel microfluidic valve. The study provides a more accurate and adoptable model for future design of new pH-sensitive hydrogel valves, and also gives a useful guideline for further studies on hydrogel fluidic applications.