Optical biosensors based on noble nanostructures currently receive attention due to their highly efficient, simultaneous analysis of a number of important biomolecules from proteomics to genomics. In this report, the combination of localized surface plasmon resonance (LSPR) with interferometry in the relative reflected intensity (RRI) spectrum of the gold capped oxide nanostructure was thoroughly exploited for label-free detection of aptamer-protein interactions. The fabrication of gold capped oxide nanostructure involved the deposition of gold on the surface of porous anodic alumina (PAA) layer chip. This novel nanomaterial enabled to simultaneously monitor the changes in both LSPR and interferometric characteristics since the biomolecular interactions occur. After immobilizing the aptamer I on the chip surface, our sensor could be applied easily for specific detection of thrombin and aptamer II with a limit of detection of 1 nM thrombin in the sample. Our optical biosensing devices connecting with the gold capped oxide nanostructure has a high potential to highly sensitive monitoring the other biomolecular interactions, such as protein-protein interactions, DNA-protein interactions, DNA-DNA hybridizations, and ligand-receptor with a massively parallel detection capability in a high-throughput system.