The Large High Altitude Air Shower Observatory (LHAASO) has three sub-arrays, KM2A, WCDA and WFCTA, located at 4410 m above sea level in Sichuan Province, China. The high-altitude location and the frequent occurrence of thunderstorms, made LHAASO suitable to study the effects of atmospheric electric fields (AEFs) on secondary cosmic rays. By analyzing the data of KM2A, the flux variations of cosmic ray air showers during thunderstorms are studied. The number of shower events that meet the KM2A trigger conditions increases significantly in
thunderstorm fields, with the maximum value exceeding 20%. The variations of trigger rates (increases or decreases) are found to be strongly dependent on the primary zenith angle. To understand the shower rate changes, the flux variations of ground-level secondary particles are analyzed. We find the average number of particles per shower event increases significantly in strong fields. Due to the acceleration by AEFs, the number of secondary particles with energy above the detector threshold increases, and then more shower events satisfy the trigger conditions, resulting in the shower rate increases. At the same time, the secondary particles carrying positive and negative charges will be deflected in opposite direction in AEFs, and this effect increases with
the zenith angles. As a result, the flux variations of shower events detected by KM2A are correlated to the primary direction.