A method for preventing overheating of a microwave oven includes receiving information of a cooking condition and a cooking start command for current cooking, the cooking condition including a magnetron output level and a current cooking period, confirming pause duration from when preceding cooking was finished to when the current cooking is started, if it is determined that the magnetron output level is a preset magnetron output level or more, and determining a basic output period and a reference period for changing the magnetron output level corresponding to the confirmed pause duration, followed by operating the microwave oven at the preset magnetron output level after changing the magnetron output level to the preset magnetron output level, if it is determined that a driving period for changing the magnetron output level has passed the determined reference period.