In traditional binary frequency shift keying (2FSK) modulation, broad sidebands in the microwave signal indirectly impact alkali metal atom transitions at different optical frequencies, which will limit the accuracy of coherent population trapping (CPT) atomic clock. This paper proposes a microwave modulation method based on discrete sine wave frequency modulation (DSWFM), which uses direct digital modulation for dynamic carrier hopping, significantly narrowing the spectral sidebands. The measured results show that compared with the traditional 2FSK modulation, the frequency stabilities of CPT atomic clock at 1 s, 10 s, and 100 s intervals based on DSWFM modulation are improved by about 17%, 36% and 48%, respectively.