We propose a biocompatible hybrid photonic platform incorporating a 3D silk inverse opal (SIO) crystal and a 2D plasmonic crystal formed on the top surface of the SIO. This hybrid photonic-plasmonic crystal (HPPC) structure simultaneously exhibits both an extraordinary transmission and a pseudo-photonic band-gap in its transmission spectrum. We demonstrate the use of the HPPC as a refractive index (RI) sensor. By performing a multispectral analysis to analyze the RI value, a sensitivity of 200,000 nm·Δ%T/RIU (refractive index unit) is achieved.