In pencil beam scanning (PBS) proton therapy, accurate monitoring of the center position and transverse size of the proton beam at the exit of the scanning nozzle is essential to ensure the safety of treatment. Since the beam spots are very small relative to the detected area in clinical applications, an improved Gaussian fitting method was proposed in this study, which extracts only the meaningful strip data beyond the specified noise threshold according to the average power of the background noise. This not only improves the accuracy, but also reduces the amount of computation. By simulation test in MATLAB, when the signal-to-noise ratio (SNR) is higher than 20dB, the accuracy of the beam position is better than 0.2mm, and the relative error of the beam size is better than 2%, and the computing time of algorithm is less than 0.4ms. Through experiments, the accuracy of the proposed algorithm in fitting the beam position was verified, and it is demonstrated that this method still works when the beam irradiates at the edge of ionization chamber.