Although the numerous advantages of polymer optical fiber (POF) sensors have been applied in different fields, the measurement consistency and sensitivity of POF evanescent wave (EW) sensors are still affected by its thermal stability and water absorption. Therefore, we perform a study to demonstrate the mechanism of the effect of heat treatments on physical and optical properties of POF EW sensors. We investigate the surface morphology, composition, refractive index, geometry, and weight of the fiber-sensing region subjected to water and vacuum heat treatments. We examine the spectral transmission and transmitted light intensity of POF sensors. We present a theoretical investigation of the effect of heat treatments on the sensitivity of POF EW sensors. The performance of the prepared sensor is evaluated using glucose and Chlorella pyrenoidosa analytes. We discovered that the spectral transmission and transmitted light intensity of the fibers shows little effect of vacuum heat treatments. In particular, the sensors, which subject to vacuum heat treatment at 110 °C for 3 h, exhibit temperature-independent measuring consistency and high sensitivity in glucose solutions in the temperature range 15-60 °C and also show high sensitivity in Chlorella pyrenoidosa solutions.