Following the outbreak of Operation Barbarossa in June 1941, Polynin served as commander of the 13th Bomber Aviation Division on the Western Front. In the most difficult conditions of the first months of the war, without proper air cover, his unit actively fought the advancing German forces in the Battles of Białystok–Minsk and Smolensk, while suffering significant losses. From August 1941, he was appointed as the commander of the Air Force units at the Bryansk Front, during which he participated in the Roslavl–Novozybkov Offensive and in the Battle of Moscow. In May 1942, he was appointed as Deputy Commander of the 2nd Air Army at Bryansk Front, and from September 1942, he was assigned as Deputy Commander of the 6th Air Army of the Northwestern Front and in 1943, he was appointed as commander of the 6th Air Army. In February 1944, the unit was assigned to the 2nd Belorussian Front and took part in the battles of Demyansk, Starorusskaya, Nevel, Polesskaya, and Operation Bagration.