With the emergence of nanobubble research, nanobubble distribution morphology at the interface and its stability control become the bottlenecks of nanobubble resistance reduction applications. In this paper, the evolutionary behavior of nanobubbles on smooth and step HOPG surfaces was compared through molecular dynamics studies. The results show that the surface energy barrier provided by the step HOPG surface restricts diffusion of gas molecules. Then, a method of multisolvent evaporation for preparing hydrophobic nanoindent surfaces was proposed, which can achieve phase separation through different evaporation rates of multisolvents, thus realizing the preparation of surface structures with uniform distribution of nanoindents. In this paper, the nucleation processes of nanobubbles on PS nanoindent hydrophobic surface, HOPG flat hydrophobic surface, and HOPG nanostep hydrophobic surface were compared by using atomic force microscopy in liquid experiment. The evolution of the volume and distribution morphology of nanobubbles on the three nanostructures was observed by 24 h in situ tests, revealing that the energy barrier effect arising from the uneven surface structure can effectively prevent adjacent nanobubbles from merging in close proximity to each other. It is also pointed out that the hydrophobic nanoindents prepared by using the multivariate solvent evaporation method in this paper can cover most of nanobubbles for stable adsorption. It can be seen from the results that the volume drop of the nanobubbles on the HOPG flat hydrophobic surface is 27% and that on the HOPG nanostep and the PS nanoindent hydrophobic surface it is reduced to 19% and 3% under the effect of structural energy barriers, respectively. The density of the nanostructures determines whether the existence of nanobubbles is stable. The coverage of nanobubbles on the HOPG flat hydrophobic surface was 3.313% when the existence of nanobubbles was mostly stable. The HOPG nanostep and PS nanoindent sizes were positively correlated with the morphological size of the nanobubbles, which increased the coverage of the nanobubbles on the hydrophobic surface of the HOPG nanostep and PS nanoindent to 5.229% and 4.437%, respectively, when the existence of nanobubbles was mostly stable.