The YCa4O(BO3)3(YCOB) piezoelectric crystal has been actively studied for high temperature sensor applications in the last few years. In this paper, the structure stability and electro-elastic properties of the YCOB crystal annealed in a harsh environment (high temperatures of 600-1100 °C and a low atmospheric pressure of 2 × 10-5atm for 24 h) were studied. The chemical bonding energy of the annealed YCOB crystal was studied, with variations being less than 0.2 eV, showing the high stability of the electronic structure in the YCOB crystal. The energies of vacancy formation (EVF) for Y, Ca, O, and B atoms were analyzed via first principles calculation. The O atoms were found to possess the lowest EVF value, being easier to escape (annealing in critical conditions) and compensate (thermal treatment at elevated temperatures in air) when compared to other atoms, thus leading to oxygen vacancy defects and a decrease in the chemical bonding strength after the annealing process. This is deemed to be the main factor dominating the electro-elastic property changes and their recovery behaviours.