Decellularized tissues are promising materials that mainly consist of extracellular matrices (ECMs) obtained by removing all cells from organs and tissues. High hydrostatic pressure (HHP) has been used for decellularization to remove cells physically from organs or tissues rather than by chemical methods. However, ultrahigh pressure induces denaturation of the ECM structure. In this study, we examined the effects of cyclic HHP at low and high pressures on the cell membrane structure to establish a novel decellularization method that enables decellularization without the denaturation of the ECM. A decellularization device using cyclic HHP (maximum pressure: 250 MPa, cycle number: 5) was developed. NB1RGB cell suspension was injected into a plastic bag to be subjected to cyclic HHP. After applying cyclic HHP, the amount of DNA inside the cells and the morphological changes of the cells were evaluated. As a result, the amount of DNA inside the cells decreased after the cyclic HHP compared to the static HHP. In addition, cyclic HHP was suggested to promote the destruction of the cell and nuclear membrane. In conclusion, it was revealed that the cell structure could be denatured and destroyed by cyclic HHP at a lower level than that of previous approaches.