With the advancement of meteorology modernization, automatic weather station had become an important means of atmospheric sounding. Collecting data and information security were basic requirements for meteorological monitoring and forecasting. When lightning struck large scale and very large scale integrated circuits, the automatic station can be damaged or its data collector can be interrupted. Two-level SPD lightning protection system and three-level ferrite lightning protection system can compensate for the lack of lightning protection board and power protector. MATLAB simulation analysis shows that the three level lightning protection circuits with ferrite are better than the two level SPD circuits in guaranteeing the automatic station operation. Putting the ferrite rings around the power lines or communication lines, along with the common lightning protection devices, can make the load terminal voltage limit to 500V. The lightning current is significantly reduced by using the simple method in the collector.