In a method of controlling an effusion cell in a deposition system, including a crucible, a guiding pathway and an injection nozzle, a guiding pathway and an injection nozzle are heated. The crucible is heated after heating the guiding pathway and the injection nozzle. In addition, in cooling the effusion cell including a crucible, a guiding pathway and an injection nozzle, the crucible is cooled. The guiding pathway and the injection nozzle are cooled after cooling the crucible. This method has an advantage of enhancing uniformity of the organic layer formed on the substrate by preventing the clogging of the injection nozzle by deposition material vaporized in the crucible or splashing.