A detailed theoretical model is provided to analyze the effects of temperature on prism-based surface plasmon resonance (SPR) sensors, including temperature dependence of the metal and prism. A complete sensitivity matrix simultaneously measures variations in refractive index (RI) and temperatures using measurements at two wavelengths for the angular-interrogation mode, or at two angles of incidence for the wavelength-interrogation mode. Correction of matrix coefficients improves accuracy of the two modes. Validation is performed using a self-designed wavelength SPR system with an adjustable incident angle perform. This method provides a new way to detect the RI and may lead to the better design and fabrication of prism-based SPR sensors.