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The phase field crystal method is used to simulate the healing process of the central gap of 3-dimensional BCC crystal material under compression strain at the atomic level. It is found that during the healing process of the central gap, the gap protrudes at both ends of it, leading to dislocation nucleation and vacancy formation. Then, by means of dislocation nucleation and dislocation emission mechanism at both ends of the gap, the thickness of the gap is reduced by one layer of atoms, and the atomic layer on the gap surface shrinks towards each other. Through the mechanism of dislocation nucleation and dislocation emission, the thickness of gap is reduced layer by layer, and finally the connection and closure of the lattice atoms on up and down surface of the gap is achieved, and the surface healing of the central gap is realized. According to the sharpening and passivation mechanism of the lattice atomic planes at both ends of the gap, the elliptic shape gap is approximated to calculate and analyze the influence of the change of stress intensity factor during the gap healing, and the critical condition of the gap dislocation emission is determined.