A security pulse generator and methods thereof are applied in fuel dispensers. The fuel dispenser includes a flow measuring transducer and a control main board on which there is a measuring microprocessor on the control main board. The security pulse generator includes: a pulse signal generating component, which generates a corresponding pulse signal according to the rotation of the flow measuring transducer; an encoding microprocessor, which receives and transduces the pulse signal, transmits it to the control main board, and meanwhile encodes the output pulse signal; a measuring microprocessor, which receives and decodes output pulse number encoded data from the encoding microprocessor and transforms it to the output pulse number after decoding it, then compares it to the pulse number of the control main board to determine if there is suspecting frauds in the fueling process.