Skyrmion, a local bubble-like topological magnetization structure, can collectively emergent in magnets in a lattice form skyrmion crystal (SkX). SkX has great application potential in functional devices because it can manipulate material properties via coupling with atomic lattices. The lattice defects such as vacancy widely exist in the SkX as well, and they have rich dynamic behaviors and have great implications for the host material. However, although the nature of ideal SkX is well studied, the characteristics of SkX defects are relatively underdeveloped. Here, we deeply studied the structural properties of a vacancy defect in the SkX by a thermodynamic phase-field simulation. We found that the higher external magnetic and temperature fields favor rigid skyrmions (crystal), in which the SkX vacancy is less deformed, while the lower fields favor softer skyrmions where the SkX vacancy structure is considerably deformed. Such unique deformation and stability of the SkX vacancy are mainly the results of the competition between free energies in the view of thermodynamics. Our study demonstrated that the external field-controlled static properties of SkX vacancy highly depend on the quasiparticle nature of skyrmions. This indicates the properties of SkX defects can be controlled by the SkX features under different fields, which should open an avenue for the study and design of smart materials and advanced devices by engineering skyrmion crystals.