This paper presents a theoretical investigation of a novel holey fiber (Photonic Crystal Fiber (PCF)) multi-channel biosensor based on surface plasmon resonance (SPR). The large gold coated micro fluidic channels and elliptical air hole design of our proposed biosensor aided by a high refractive index over layer in two channels enables operation in two modes; multi analyte sensing and self-referencing mode. Loss spectra, dispersion and detection capability of our proposed biosensor for the two fundamental modes (HE11(x) and y11 HE11(y) ) have been elucidated using a Finite Element Method (FEM) and Perfectly Matching Layers (PML).