In the low As beam equivalent pressure condition, the in-situ annealing treatment is carried out for the previously atomically flat GaAs(001) βup 2(2×4) reconstruction surface. Utilizing scanning tunneling microscopy, the surface is found to change its morphology simultaneously with the surface reconstruction during the increase of low As beam equivalent pressure annealing time. The surface morphology undergos from ordered flat to disordered flat and then gradually returns to the ordered flat state again. The surface reconstruction turns from βup 2(2×4) to (2×6) and then changes to “zig-zag” (2×6) state. And there is a correlation between the evolution of the surface morphology and surface reconstruction.