A controller of an isolated switching converter includes an error amplifying circuit, a modulation signal generator, a first comparison circuit, a primary off detection circuit, a secondary logic circuit, an isolation circuit and a primary logic circuit. The error amplifying circuit generates a compensation signal based on the difference between a reference signal and a feedback signal. The first comparison circuit compares the compensation signal with a modulation signal generated by the modulation signal generator and generates a first comparison signal. The primary off detection circuit detects whether the primary switch is off and generates a primary off detection signal. The secondary logic circuit generates a secondary control signal to control the secondary switch based on the first comparison signal and the primary off detection signal. The isolation circuit receives the first comparison signal and generates a synchronous signal electrically isolated from the first comparison signal. The primary logic circuit generates a primary control signal to control the primary switch based on the synchronous signal.