The invention discloses a granary lateral ventilation method and a system thereof. In the invention, a ventilation tunnel is arranged on the inside wall of the granary which covers a sealing film on the surface of grain, lateral ventilation is carried out on all grain piles in the granary. Compared with cage on the ground and geosyncline vertical ventilation system in the granary, the ventilation tunnels are small in quantity, ventilation way ratio is small, ventilation uniformity is good, ventilation dead corner is hardly existed, ventilation efficiency is high and energy consumption is low. Besides, installation or disassemble of cage on the ground for transporting the grain in and out in the prior art is avoided. The grain terrace is not provided with a ventilation tunnel in any form and the terrace is complete, thus being convenient for mechanized grain transportation, lowering the labor intensity of grain transporter and saving time for grain transportation.