A general method for assembling patterned interfaces of uniform, flexible mesoporous iron oxide nanopyramid islands (NPIs) is presented. The three-dimensional (3D) mesoporous iron oxide-NPI interfaces possess a unique mesostructure that features a large surface area (~158m2 g - 1), a large pore size (~18 nm) and excellent flexibility (can be folded 100 times). Furthermore, the 3D mesoporous Au-NPI interfaces allow efficient immobilization of cytochrome c (Cyt c; more than 165-fold increase) and a significant enhancement of localized surface plasmon resonance (~26-fold at 625 nm) compared with that of two-dimensional (2D) planar iron oxide films without nanopores. More importantly, the ultrasensitive integrated interfaces demonstrate over 1000-fold enhancement of the photocurrent variation on the 3D mesostructures based on the switchable direct electrochemistry of Cyt c. The strategy of interfacial assembly offers new possibilities for the chemical design of patterned mesoporous semiconductors with high flexibility and tailored photocatalytic characteristics. This investigation provides a novel paradigm for an unconventional 3D porous biointerface that can be used for sub-nanomolar level recognition of biomolecules (~0.2 nM for H2O2) and suggests the new concept of large-surface-area 3D mesostructure-protein interfaces as a step toward using direct electrochemistry for biomedical applications.