The inductively coupled plasma etching parameters for fabricating sensing windows of integrated Mach–Zehnder interferometer sensor based on polymers are systematically investigated. Under the optimum etching condition, we fabricate an improved sensing waveguide with three sensing surfaces, whose sensitivity can be enhanced by a factor of 3.5 in theory. Through precisely controlling the etching time, low propagation loss and high hydrophilicity are both achieved in the etched sensing waveguide. This optimizing approach along with rapid response and stable operation has rendered the MZI waveguide sensor more competent to practical requirements of RI sensing and biochemical sensing.