This study demonstrates a low crosstalk temperature-compensated fiber-based urea sensor based on the hybridization of surface plasmon resonance (SPR) and Mach-Zehnder interferometer (MZI). In this sensing structure, an inscribed waveguide and a semi-open cavity are processed by a femtosecond laser in an optical fiber to excite an SPR signal sensitive to refractive index (RI) and an MZI signal highly sensitive to temperature. Based on the temperature detected by the MZI, the influence of temperature on the SPR signal’s RI detection can be calculated and compensated for using a sensitivity matrix. Based on this precise RI detection of the SPR signal, we have achieved selective urea detection by bio-functionalizing the sensor surface using the urease self-assembly method. The sensitivity and limit of detection for urea are 7.98 (nm/mmol/L) and 0.13 mmol/L, respectively, which are better than those in previous studies. Compared to previous temperature compensation studies, this SPR + MZI sensing method using femtosecond laser processing significantly improves the temperature sensitivity of the MZI signal, which reduces crosstalk and ensures a sufficient working range for the SPR signal. Therefore, this sensor is crucial for advancing high-precision temperature compensation detection, high-sensitivity biological detection, and the future application of the femtosecond laser technology.