Mechanical properties of red blood cells (RBCs) change during their senescence which supports numerous physiological or pathological processes in circulatory systems by providing crucial cellular mechanical environments of hemodynamics. However, quantitative studies on the aging and variations of RBC properties are largely lacking. Herein, we investigate morphological changes, softening or stiffening of single RBCs during aging using an in vitro mechanical fatigue model. Using a microfluidic system with microtubes, RBCs are repeatedly subjected to stretch and relaxation as they squeeze into and out of a sudden contraction region. Geometric parameters and mechanical properties of healthy human RBCs are characterized systematically upon each mechanical loading cycle. Our experimental results identify three typical shape transformations of RBCs during mechanical fatigue, which are all strongly associated with the loss of surface area. We constructed mathematical models for the evolution of surface area and membrane shear modulus of single RBCs during mechanical fatigue, and quantitatively developed an ensemble parameter to evaluate the aging status of RBCs. This study provides not only a novel in vitro fatigue model for investigating the mechanical behavior of RBCs, but also an index closely related to the age and inherent physical properties for a quantitative differentiation of individual RBCs.