DNA/GO functional structures have been widely used in biosensors, biomedicine and materials science. However, most studies about DNA/GO functional structures do not take into account the coexistence of both large unoxidized and oxidized regions on GO sheets. This special local structure provides the boundary region, which is the junction area between unoxidized and oxidized regions, and exhibits a special amphiphilic property of the GO sheets. Here based on molecular dynamics simulations, our results predict that the adsorption efficiency of long strand ssDNA molecules adsorbed on GO is 43%. Further analysis has shown that the ssDNA adsorption behaviors on the GO surface are more likely to start in the boundary region, even for 20 mer ssDNA molecules. Looking into the adsorption dynamic process we can see that the hydrogen bonds between ssDNA and GO are very active and easily broken and formed, especially for the boundary region of the GO surface, resulting in easy capture and adsorption of the ssDNA molecules on this region. The result provides insightful understanding of the adsorption behavior of ssDNA molecules on this amphiphilic GO surface and is helpful in the design of DNA/GO functional structure-based biosensors.