The present invention provides an isolated power supply circuit with a programmable function and a control method thereof. The isolated power supply circuit includes: a transformer circuit, a power switch circuit, a control circuit, and a discharge circuit. The control circuit generates an operation signal and a bleeding signal according to a setting signal. The discharge circuit is coupled to an output node, for generating a discharging current. When the programmable output voltage at the output node switches between different predetermined levels, in a transition period, the bleeding signal adjusts the discharging current to discharge the output node, such that the transition period is shortened.