A manufacturing method of a fluid control device is provided. Firstly, a housing, a piezoelectric actuator and a deformable substrate are provided. The piezoelectric actuator includes a piezoelectric element and a vibration plate having a bulge. The deformable substrate includes a flexible plate and a communication plate. The flexible plate includes a movable part. Then, the flexible plate and the communication plate are stacked on and coupled with each other to form the deformable substrate. Then, the housing, the piezoelectric actuator and the deformable substrate are sequentially stacked on each other and coupled with each other. A synchronous deformation process is implemented by applying at least one external force to the deformable substrate, so that the flexible plate and the communication plate of the deformable substrate are subjected to a synchronous deformation, and a specified depth between the movable part and the bulge of the vibration plate is defined.