Integration of optical devices onto silicon substrate is attracting increasing attention in the field of optoelectronics. The fluidic self-assembly technology was applied to the integration of thin-film metal-semiconductor-metal(MSM) photodetector, the integration results was related to the geometry of the binding site. The spacing and shape of the binding sites on the thin-film MSM photodetector will affect the integration process of device onto the host substrate. In order to effectively predict the effect, MATLAB was used to simulate the distribution of interfacial free energy for the integration process. Firstly, based on the introduction of thin-film MSM photodetector and its integration, a model of translation and rotation during the integration was established for the simulation. Then, according to the linear relationship between the interfacial free energy and the matching degree, the distribution of the matching degree was investigated for the different binding sites with the different spacing and shape. By analyzing the relationship between the slope of the matching degree and the correct-assembly/false-assembly state, it predicted that the integration results would be better when the spacing between the binding sites is longer and the shape of the binding sites is trapezoid. Finally, considering that the thin-film optical devices may have specific requirment of positive and negative contacts, the binding sites with asymmetric shape was designed to avoid the reverse binding connection during the integration process.