Accurately manipulating quantum states is a fundamental strategy for improving the performance of quantum metrology, computing, and simulation. However, the quantum state is susceptible to dephasing due to the temperature and density of the atomic ensembles. In this paper, we experimentally study the effect of Floquet engineering (FE) on the dephasing process in an 87Sr optical clock. By measuring the Rabi flopping process under different temperatures of the cold ensemble and numbers of atoms trapped in the lattice, our results show that the FE can suppress the dephasing due to high temperatures or a large number of atoms. Indeed, when the temperature and the number of atoms are 3.8 μK and 6300, respectively, the FE can obviously suppress the dephasing effect and improve the maximum excitation fraction of the Rabi spectrum by 15.4%.