<p>In atomic force microscope (AFM) indentation experiment, the flexibility of AFM cantilever has profound impact on behaviors of nanoindentation. However, the cantilever stiffness dependent on nanoindentation properties has not been thoroughly resolved. In this paper, we establish a nanoindentation system composed of spring-indenter and molybdenum disulfide supported/suspended substrate, the deformation of the indenter is simulated by spring stiffness. The actual velocity of the indenter is determined based on the complexity of the indentation interface, which is the same as the motion state of the AFM indenter. The nanoindentation processes with different cantilever stiffnesses and temperatures are monitored by the indentation force, dissipated energy, and phonon spectrum. For both supported and suspended substrates, greater stiffness can lead to substrate fracture more quickly due to faster energy dissipation. The depth of substrate damage becomes shallower in higher temperature, and the time of system collapse also becomes shorter. Distinct phononic properties are further observed between these two substrates. Indenting a suspended substrate is equivalent to applying tensile strain to the substrate, thus longer duration of indentation can lead to a red shift in phonon density of states. In contrast, the corresponding supported substrate has lower interlayer distance and higher force constant, resulting in a blue shift of phonon spectra.</p>