A strain-insensitive optical fiber Mach–Zehnder interferometer (MZI) composed of a rectangular micropore and refractive index modification waveguide (WG) is proposed, which realizes simultaneous measurements of seawater temperature and salinity. The micropore transversely penetrates the single-mode fiber, which is fabricated by ablating part of the cladding and core with the femtosecond laser. The WG is constructed by inscribing successive modified lines in the fiber cladding by laser direct writing technology. The phase difference between interference beams changes with the temperature and salinity variations, which causes the shift of characteristic wavelengths. The maximum response sensitivities are 3.205 nm/°C and −2.714 nm/ ‰, with resolutions of 0.006 °C and 0.007 ‰. To solve the crosstalk problem between these two seawater parameters, a quadratic polynomial surface fitting method is utilized to achieve accurate data decoupling and reduce measurement errors. In addition, the experimental tests show that the compact MZI sensor is insensitive to longitudinal strain, and has good measurement repeatability and stability, which has broad application potential in the dynamic and complex detection of the marine environment.