The micro-patterned topography can affect bacterial enrichment and selective distribution by modifying the characteristics of material surface. In this study, we fabricated microcavity patterned silicon surfaces, and quantitatively explored the amount and distribution of Escherichia coli (E. coli) cells attached on a series of defined topographies. The results showed that E. coli cells enrichment was significantly increased on silicon nanowires-based microcavity array when compared to nanowires patterned silicon wafer. Furthermore, the microcavity diameter can control bacterial distribution by changing hydrophilic performance of interface. With the microcavity diameter of 7 µm, the cells colonized into the microcavity almost in its entirety, whilst distributed around the microcavity completely with 10 µm diameter, regardless of centre distances. This phenomenon can be explained by the Cassie-Baxter model equation according to the wettability. The distribution of bacterial enrichment changed with the silicon surfaces turning from non-wetting status to wetting status when treated with oxygen plasma to modify the hydrophobicity. These results demonstrated that microcavity patterned surface could favor bacterial enrichment on silicon and strictly confined bacterial distribution inside/outside the microcavity. Moreover, the nanowires inside microcavity can also increase electron conductivity and reduce the internal resistance, thus providing scientific evidence for the design of wearable microbial fuel cell with rational optimization and integration of different components for electronic skin.