The invention relates to methods for adaptive clock reconstruction and decoding in audio frequency. The method includes the steps of: receiving a modulated signal, wherein the modulated signal is modulated by RC-FSK (Return to Carrier Frequency Shifting Keying); performing a spectrum analysis to the modulated signal to obtain a plurality of frequency envelopes; storing the frequency envelopes; searching the peak values of the frequency envelopes and the time points corresponding to the peak values to modify an estimated period; and generating a clock period for the RC-FSK demodulation and a clock phase for the RC-FSK demodulation according to the estimated period.