This paper addresses the degradation of imaging quality in high-resolution CubeSats caused by micro-vibrations from attitude control flywheels. It proposes a micro-vibration suppression scheme that incorporates multi-disciplinary integrated modeling, dual passive vibration isolation, and multi-level verification. A comprehensive model encompassing flywheel disturbance, optics, attitude control, and structure is developed to elucidate the transmission dynamics of micro-vibrations from the source to the optical payload. A dual suppression system utilizing silicone rubber isolators is engineered for both the disturbance source (flywheel) and the payload (optical camera). By optimizing stiffness matching and damping, it achieves a balance between isolation efficiency and stability in attitude control. A three-tier verification system comprising “numerical simulation–ground microgravity testing–on-orbit imaging” has been established. The findings indicate that the dual isolation system diminishes the pixel offset amplitude of the optical payload to under 0.1 pixels (down to the 0.02 pixel level in the high-frequency band), with an isolation efficiency of 80%. Consistent outcomes from terrestrial and orbital validation affirm the engineering viability of the plan. This research offers theoretical backing for the precise control of micro-vibrations in micro-nano satellites, thereby enhancing their utility in high-resolution remote sensing applications.