<p>Beyond hardware improvements, Floquet Engineering (FE), as a widely used Hamiltonian engineering method, offers new levels of control and promising opportunities for enhancing optical lattice clock performance. However, while FE shapes novel Hamiltonians, its time-periodic nature introduces micromotion, leading to periodic disturbances in the system, such as frequency shifts. In this work, we introduce a dual-modulation (DM) FE method, simultaneously driving the lattice and probing lasers, allowing independent control of atomic motional and electronic degrees of freedom. Using this framework, we theoretically predict and experimentally observe the micromotion shifts. Additionally, by tuning the DM modulation parameters appropriately, we can fully eliminate the Doppler shift caused by the lattice laser modulation. Building on this Doppler-free synchronization modulation, we observe the dynamic localization of atoms in a shallow lattice while eliminating the periodic interference from Doppler shifts.</p>