As for the problem that the non-stationary fluctuating wind induces dramatic changes of atmosphere refraction at tens of meters height above the rough ocean surface,which reduces the accuracy of orbit measurement and control system while tracking spacecraft at low elevation.A new atmosphere refraction modification method is investigated based on the modified Monin-Obukhov approximation,with the consideration of the influence by random rough ocean surface which is established by Monte-Carlo method.Experimental results of several in-orbit spacecraft measurement data indicate that precision can be dramatically improved compared with traditional methods.