To address the temperature cross-talk issue in detecting heavy metal ions in natural waters, a highly-integrated and fully fiber-optic metal ion sensing system capable of temperature-concentration decoupling measurement has been designed. This system integrates a fluidic detection structure assisted by side-polished fibers (SPFs) with a Sagnac interferometer. By selecting common refractive index ranges of contaminated water sources and common environmental temperature ranges, numerical simulations were conducted to analyze the sensing characteristics of the photonic bandgap boundary and interference spectrum wavelength in relation to these two parameters, and finally, a temperature and refractive index decoupling model was obtained. Results show that this system successfully demodulates the temperature parameter in solution refractive index sensing, exhibiting a concentration sensitivity of −355.96 nm∙mL/mol and a temperature interference of −2.03 nm/°C.