In this study, a new method for the simulation of the time-dependent behavior of actin cytoskeleton during cell shape change is proposed. For this purpose, a three-dimensional model of endothelial cell consisting of cell membrane, nucleus membrane, and main components of cytoskeleton, namely actin filaments, microtubules, and intermediate filaments is utilized. Actin binding proteins, which play a key role in regulating actin cytoskeleton behavior, are also simulated by using a novel technique. The actin cytoskeleton in this model is more dynamic and adoptable during cell deformation in comparison to previous models. The proposed model is subjected to compressive force between parallel micro plates in order to investigate actin cytoskeleton role in cell stiffening behavior, nucleus deformation, and cell shape change. The validity of the model is examined through the comparison of the obtained results with the data presented in previous literature. Not only does the model force deformation curve lie within a range of the experimental data, but also the elastic modulus of the cell model is in accordance with former studies. Our findings demonstrate that augmentation of actin filaments concentration within the cell reduces force transmission from cell membrane to the nucleus. Furthermore, actin binding proteins concentration increases by the enhancement of cell deformation and it is also indicated that cell stiffening with an increase in applied force is significantly affected by actin filaments reorientation, actin binding proteins reorganization and actin binding proteins augmentation.