A controller with leakage current protection of a diode includes a comparison unit, a reference voltage generation unit, a time out signal generation unit, and a gate signal generation unit, wherein the diode is applied to a secondary side of a power converter. The comparison unit outputs a corresponding selection signal according to a compensation voltage and a threshold. The reference voltage generation unit outputs a corresponding reference voltage range according to the corresponding selection signal. The time out signal generation unit determines a corresponding time out according to the corresponding selection signal, and generates a corresponding time out signal when a voltage corresponding to an auxiliary winding has no peak to cross an upper limit of the corresponding reference voltage range during the corresponding time out. The gate signal generation unit enters the leakage current protection or a quasi-resonant mode according to the corresponding time out signal.