A clock generating apparatus and a fractional frequency divider thereof are provided. The fractional frequency divider includes a frequency divider (FD), a plurality of samplers, a selector and a control circuit. An input terminal of the FD is coupled to an output terminal of a multi-phase-frequency generating circuit. Input terminals of the samplers are coupled to an output terminal of the FD. Trigger terminals of the samplers receive the sampling clock signals. The input terminals of the selector are coupled to output terminals of the samplers. An output terminal of the selector is coupled to a feedback terminal of the multi-phase-frequency generating circuit. The control circuit provides a fraction code to a control terminal of the selector, so as to control the selector for selectively coupling the output terminal of one of the samplers to the feedback terminal of the multi-phase-frequency generating circuit.