The water fraction of gas-water flow can be measured by a microwave-based approach, but the measurement is unstable if water conductivity is changed. To overcome this, the present study proposes an on-line water fraction measurement method taking advantages of a microwave transmission line sensor. An equivalent circuit and a two-port network are established to reveal that, in a high conductivity environment, the sensor’s S21 phase is linearly related to phase constant and can measure the water fraction. Considering an air-water stratified flow, we conduct experimental and numerical investigations on the variation of the phase against conductivity and water fraction. It is found that 3.31–8.52 S/m conductivity has no effect on the phase. Subsequently, experimental and numerical models are developed for predicting 0–100% water fraction. Both absolute errors are within 2.2% at 95% confidence probability. The simulation method is a low-cost alternative of traditional gas-water flow testing.