The effects of changes in the solar radiative emission on ozone levels in the stratosphere have been considered as a candidate to explain the link between solar activity and its effects on the climate. As ozone absorbs electromagnetic radiation, changes in ozone concentrations alter Earth's radiative balance by modifying both incoming solar radiation and outgoing radiation. In this way, ozone controls solar energy deposition in the stratosphere and its variations alter the thermal structure of the stratosphere. These changes are assumed to propagate downward through a chain of feedbacks involving thermal and dynamical processes. The effects of high energy particle precipitation on mesospheric and stratospheric ozone have also been investigated. However, while the effects of high energy particle precipitation on ozone distribution in the auroral region has been investigated during the last decades, little is known about the role of the high energy particle precipitation on the stratospheric composition and thermal structure in the tropical/subtropical region. Here we show that the spatial distribution of the lower stratosphere temperature is affected by the presence of the southern hemisphere magnetic anomaly. We found that during the austral winter and spring, in the subtropical region (below 30 deg S), the reduction of the lower stratosphere temperature occurs systematically in the magnetic anomaly area. This result is consistent with the observations that in the southern hemisphere subtropical region the energy of precipitating particles is deposited lower in altitude in regions with weaker magnetic field intensity.