Annihilation process of a pair of vortices in holographic superfluid is numerically simulated. The process is found to consist of two stages which are amazingly separated by vortex size . The separation distance between vortex and anti-vortex as a function of time is well fitted by $\alpha (t_{0}-t)^{n}n=1/2\delta (t)>2rn=2/5\delta(t)<2r$. Then the approaching velocity and acceleration as functions of time and as functions of separation distance are obtained. Thus the attractive force between vortex and anti-vortex is derived as for the first stage, and $f(\delta)\propto 1/\delta^{4}$ for the second stage. In the end, we explained why the annihilation rate of vortices in turbulent superfluid system obeys the two-body decay law when the vortex density is low.

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