A two-dimensional triangular lattice solid/fluid phononic crystal (PnC) is proposed as a sensitive biosensor to detect the temperature of the Methyl Nonafluorobutyl Ether (MNE) in the range of 10–40 °C. Temperature changes in MNE represent an important issue for its various applications. Indeed, the MNE is widely used in cosmetic and beauty products for its non-toxic, non-flammable, and colorless chemical properties. For this purpose, a sensitive biosensor for temperature and physical properties of MNE appears necessary. The PnC biosensor consists of a triangular lattice of tungsten cylinders embedded in an epoxy background inside of which a line of hollow cylinders filled with MNE is introduced as a waveguide for guiding resonant modes with low group velocity. We show that the PnC biosensor provides sharp guided modes in the bandgap with high quality factors and frequencies depending on the MNE temperature with high sensitivity. The introduction of damping inside the liquid shows that the shear viscosity, compared to longitudinal, affects drastically the amplitude of the resonant peaks. However, the length of the waveguide can be adapted so as to recover the resonant peak in the presence of viscosities.