A power converter with over temperature protection compensation includes a main conversion unit, a primary-side control unit, a secondary-side control unit, a secondary detection circuit, and an over temperature adjustment circuit. The secondary-side control unit obtains a secondary voltage change value through the secondary detection circuit, and the secondary-side control unit correspondingly provides a current change value to the over temperature adjustment circuit according to the secondary voltage change value. The over temperature adjustment circuit provides a temperature control voltage according to the current change value so that the secondary-side control unit determines whether an over temperature protection is activated according to the temperature control voltage.