Abstract: To raise the alarm rate of small scale and low-level turbulence detected by lidar, an alerting algorithm based on the combination of glide-path scanning and transverse velocity structure function was presented in this paper. Firstly, the scanning sector of the glide-path was divided into several overlapping subsectors, and the transverse structure function of each subsector was calculated by using the spatial fluctuation method. Secondly, the structure function was fitted with that predicted by the theoreitical Von Karman model to give eddy dissipation rate, and the results on provisions of the International Civil Aviation Organization's turbulence threshold was compared to come to the conclusion. The performance of the proposed method was verified through the lidar collecting data of Hong Kong International Airport installed by Hong Kong Observatory. The results show that the proposed algorithm detects the small scale turbulence which longitudinal velocity structure function fails to detect. The new proposed method is effective, it is significant to raise the alarm rate.