High-energy physics in the atmosphere (HEPA) has undergone an intense reformation in the last decade. Correlated measurements of particle fluxes modulated by strong atmospheric electric fields, simultaneous measurements of the disturbances of the near-surface electric fields and lightning location, and registration of various meteorological parameters on the Earth have led to a better understanding of the complex processes in the terrestrial atmosphere. The cooperation of cosmic rays and atmospheric physics has led to the development of models for the origin of particle bursts recorded on the Earth’s surface, estimation of vertical and horizontal profiles of electric fields in the lower atmosphere, recovery of electron and gamma ray energy spectra, the muon deceleration effect, etc. The main goal of this review is to demonstrate how the measurements performed at the Aragats cosmic ray observatory led to new results in atmospheric physics. We monitored particle fluxes around the clock using synchronized networks of advanced sensors that recorded and stored multidimensional data in databases with open, fast, and reliable access. Visualization and statistical analysis of particle data from hundreds of measurement channels disclosed the structure and strength of the atmospheric electric fields and explained observed particle bursts. Consequent solving of direct and inverse problems of cosmic rays revealed the modulation effects that the atmospheric electric field has on cosmic ray fluxes.