Sudden weather changes can endanger the middle and upper atmosphere lidar in observation. Hence, to ensure the safe operation of the lidar, the weather conditions of stations need to be monitored in real-time. Consequently, this paper develops an automatic weather identification system for a local weather station, using a night-sky image analyzer with digital image processing technology. Investigations reveal that the system can judge in real time whether the current weather conditions meet the lidar's observational conditions, subsequently giving an early warning when it will become bad weather in the next two hours. Furthermore, the continuous observation results of trial operations for one year show that the proposed system can meet the middle and upper atmosphere lidar automatic operation requirements with high stability and practicability.