With the experimental objects of the C3S pastes curing at 60 days with water-solid ratio of 0.5, the micro mechanical characteristic between C-S-H clusters and tip has been investigated in the low scale. The results show that the experimental method is feasible for bonding force between C-S-H clusters and tip using atomic force microscopy (AFM) in the real atmospheric conditions. Though bonding force values are discrete in view of the anisotropy character of the cement-based material, the normal distribution can be fitted for the variation of bonding force between C-S-H blusters in the C3S pastes and AFM tip with a mean of 6.2nN. Even if bonding force values is somewhat higher due to the roughness and the measuring conditions in the paper, the experimental method using AFM could still be effective for the lateral correlation for bonding force of the different systems. The research on bonding force between C-S-H clusters would play the important role in establishing the new microscopic structural model.