Hydration layers formed on charged sites play crucial roles in many hydration lubrication systems in aqueous media. However, the underlying molecular mechanism is not well understood. Herein, we explored the hydration friction of lipid bilayers with different charged headgroups at the nanoscale through a combination of frequency-modulation atomic force microscopy and friction force microscopy. The nanoscale friction experiments showed that the hydration friction coefficient and frictional energy dissipation of a cationic lipid (DPTAP) were much lower than those of zwitterionic (DPPE) and anionic (DPPG) lipids. The hydration layer probing at the surfaces of different lipid bilayers clearly revealed the relationship between the charged lipid headgroups and hydration layer structures. Our detailed analysis demonstrated that the cationic lipid had the largest hydration force in comparison with zwitterionic and anionic lipids. These friction and hydration force results indicated that the difference of the lipid headgroup charge resulted in different hydration strengths which led to the difference of hydration friction behaviors. The findings in this study provide molecular insights into the hydration friction of lipid bilayers, which has potential implications for the development of efficient hydration lubrication systems with boundary lipid bilayers in aqueous media.