A pressure control system of a wafer polishing apparatus includes a main input air pressure regulator, an air branch conduit, a plurality of first pipes, a plurality of auxiliary air pressure regulators, a plurality of second pipes, and a plurality of air pressure controlling devices. The air branch conduit is connected with the main input air pressure regulator. The first pipes are connected between the air branch conduit and the auxiliary air pressure regulators. The second pipes are connected between the auxiliary air pressure regulators and the air pressure controlling devices. Accordingly, the air pressure controlling devices can control the pressure outputted from a polishing head of the wafer polishing apparatus to a surface of a wafer.