An air-conditioning system of a substrate processing apparatus includes an air inlet line for providing air to a clean room. A contamination control apparatus for removing contaminants in the air is connected to the air inlet line. A controller controls temperature and humidity of the air without the contaminants. An air outlet line provides the air having the controlled temperature and humidity to a substrate processing chamber that is disposed in the clean room. The contamination control apparatus includes a spray unit having at least one nozzle that sprays water. At least one eliminator that traps the water for capturing contaminants in the air and drops the trapped water into a tank. A water circulation unit provides the water that includes an additive for controlling pH of the water to the spray unit.