Thunderstorm is a complex of electrical, optical, and acoustical phenomena that occurs in the troposphere layer and liberates a huge amount of energy, which diffuses the electric field, propagates atmospheric acoustic and gravity waves into the ionosphere, and changes the ionospheric parameters such as the electron density and ionospheric conductivity. In this paper, irregularities in the TEC, the activity of IGW and IAW, influenced by thunderstorm were investigated for July 2017. Our results show a direct relationship between increase in thunderstorm activities and the TEC irregularities. The average of irregularity amplitudes, under severe thunderstorm conditions was 1.3 times larger than calm conditions (non-lightning days). Further, ROTI average on high thunderstorm activity days was obtained 1.25 times larger in value, compared to calm conditions. Furthermore, the average of IGWs maximum amplitudes was 0.23 and 0.12 TECU for high and low thunderstorm activity days, respectively. Our statistical study showed clear effects of intense thunderstorms on the ionosphere, mostly with a roughly 1–2 h delay. It should be noted that solar activity and geomagnetic conditions were the same in all investigated days.