The continuing effort to utilize the unique properties present in a number of strongly correlated transition metal oxides for novel device applications has led to intense study of their transitional phase state behavior. Here we report on time-resolved coherent X-ray diffraction measurements on a single vanadium dioxide nanocrystal undergoing a solid-solid phase transition, using the SACLA X-ray Free Electron Laser (XFEL) facility. We observe an ultrafast transition from monoclinic to tetragonal crystal structure in a single vanadium dioxide nanocrystal. Our findings demonstrate that the structural change occurs in a number of distinct stages attributed to differing expansion modes of vanadium atom pairs.