We report herein the establishment of a single-cell compression method based on force measurements in atomic force microscopy (AFM). The high-resolution bright-field or confocal laser scanning microscopy guides the location of the AFM probe and then monitors the deformation of cell shape, while microsphere-modified AFM probes compress the cell and measure the force. Force and deformation profiles of living cells reveal a cubic relationship at small deformation (<30%), multiple peaks at 30-70% compression, and a rapid increase at over 80% deformation. The initial compression may be described qualitatively and quantitatively using a simple model of a nonpermeable balloon filled with incompressible fluid. Stress peaks reflect cell membrane rupture, followed by the deformation and rupture of intracellular components, beyond which the cell responses become irreversible. The Young's modulus and bending constant of living cell membranes are extracted from the balloon models, with 10-30 MPa and 17-52 kT, respectively. The initial compression of dead and fixed cells is modeled using Hertzian contact theory, assuming that the cell is a homogeneous sphere. Dead cells exhibit a cytoskeleton elasticity of 4-7.5 kPa, while fixation treatment leads to a dramatic increase in the cytoskeletal Young's modulus (150-230 kPa) due to protein cross-linking by imine bonds. These results demonstrate the high sensitivity of the single-cell compression method to the molecular-level structural changes of cells, which suggests a new generic platform for investigating cell mechanics in tissue engineering and cancer research.