The self-assembly adsorption of function protein on crystal surfaces, as a common phenomenon, broadly takes place in many applications of biosensors, biocapsules and bioMEMS/bioNEMS. To systematically investigate the different adsorption characteristic of the same function protein on two different crystal surfaces under the identical environment, a hybrid surface composing silica and discontinuous Gold Nano Film (GNF) was fabricated by Physical Vapor Deposition (PVD) and ultrasonic cleaning method, where the dynamic process of the self-assembly adsorption of Bovine Serum Albumin (BSA) was in situ observed by Atomic Force Microscope (AFM). The variations on the junction area of the two different surfaces were studied in the aqueous solution before and after injecting BSA with 0.05 mg/ml concentration. It was found that silica, compared with same hydrophilic GNF, took on a fairly weak adsorption force. The results indicated that the adsorption strength of BSA on the hydrophilic crystal surface was determined not only by hydrophilic property, but also other interaction forces, like Van der Waals and so on. Moreover, observed under the contact mode of AFM, BSA adsorbed on GNF had great tendency to forming a ridge-like topography. These results may be helpful in the application of immunosensors and other areas.