The imaginary part of the inter-quarks potential of moving heavy quarkonia is investigated in a dual supergravity of the AdS background deformed by dilaton, which induces the gauge field condensate in the dual gauge theory. We analyze the quark anti-quark pair moving transverse and parallel to the plasma wind, respectively. It is shown that for both cases the presence of D-instanton density tends to increase the inter-distance and decrease the imaginary potential, reverse to the effect of the pair's velocity. Moreover, it is found that the D-instanton density has stronger effects for the parallel case rather than transverse.