An automatic clock generation system is used for automatically outputting a sampling signal and a holding signal to an analog front end circuit and for sampling the analog signal. The clock generation system comprises a clock generator generating a plurality of clock signals and a comparing module. According to the plurality of clock signals, the comparing module compares the analog signal with a first reference signal and outputs a first comparison signal. The comparing module further compares the digital signal outputted by the analog front end circuit with a second reference signal and outputs a second comparison signal. The clock generator selectively outputs a first clock signal, corresponding to the first comparison signal, of the plurality of clock signals as the sampling signal when the first comparison signal received by the clock generator is at a high state. The clock generator further selectively outputs a second clock signal, corresponding to the second comparison signal, of the plurality of clock signals as the holding signal when the second comparison signal received by the clock generator is at the high state.