A PWM controller includes a short circuit mode circuit which has input ends connecting simultaneously to a power supply input end and an output end of an output driving circuit, and an oscillator which has a temperature compensation circuit that includes a medium value multi-transistor resistor of a negative temperature coefficient and a well resistor of a positive temperature coefficient. The invention also provides a charger circuit which includes the PWM controller set forth above and a constant voltage/current control circuit coupling with the PWM controller through a transformer. A system adopting the PWM controller circuit and charger circuit of the invention does not need a voltage stabilization diode now equipped in many conventional designs. The invention provides an improved short circuit protection and eliminates low frequency harmonic waves.