High temperature structural acoustic sensors play an important role in many applications. Fused quartz waveguide is a popular choice due to its resistance to harsh environments and its convenience of modification. However, time of flight between pulse and echo, which is widely used in these sensors, tends to encounter drifts in fast temperature changing process even after temperature returns to initial value. In this article, different annealing process are performed for a special modified fused quartz waveguide with a sensor node. Annealing treatment is found able to reduce the drift when the waveguide undergoes a sudden temperature spike to 1000 °C at 500 kHz operating acoustic frequency, and the best annealing condition could make the drift one magnitude smaller. A following temperature test up to 1000 °C shows consistent measurement readings.