Brillouin optical time domain relectometer (BOTDR) based on short time Fourier transform (STFT) algorithm can achieve fast temperature detection. However, there are frequency leakage and fence effects, resulting in poor temperature measurement accuracy. In view of the above problems, this paper builds on the STFTBOTDR temperature measurement system. Through the optimization of window function and operation point number, the frequency leakage caused by STFT algorithm is suppressed, and the accuracy of STFTBOTDR temperature measurement is improved. In the experiment, the time domain window length is set to 16 m, and the window sliding step is 05 m, which compares the measurement accuracy under different window functions and operation points. The results show that when the Hanning window is used and the number of calculation points is 1 024, the accurate detection and positioning of the temperature change of the fiber end of 96 km can be realized with an error of 1012℃. The measurement accuracy is ±25 MHz. When the window function is not used, the measurement accuracy is ±125 MHz, and accurate measurement of temperature change cannot be achieved. The research results provide a reference for the optimization of the accuracy of the STFTBOTDR temperature detection system.