We present a novel method for investigating a nanometric cluster of water molecules, which includes the formation and manipulation of nanometric water, and the measurement of its mechanical properties. The atomic force microscope based on the quartz tuning-fork sensor is employed to form and manipulate the nanometric water, and the theoretical tool of amplitude-modulation atomic force microscopy is used to obtain the elasticity, viscosity and dissipation energy of it. With high vertical resolution less than [similar]0.1 nm and high force sensitivity of [similar]0.01 N m−1, this tool facilitates the stable formation and manipulation of a nano-water cluster ([similar]104 molecules) in air without ‘jump-to-contact’ instability, as well as quantitative measurements of its physico-chemical properties.