The research of microwave absorption material has great significance for solving electromagnetic pollution and military security. Manganite perovskite has huge potential for developing into a fine microwave absorption material due to its adjustable electromagnetic property, while the mechanisms are still being explored. Therefore, we aim to explain the microwave loss mechanism of manganite perovskite with the double exchange interaction of Mn ion. Orthorhombic structure CaMnO3 was effectively synthesized, and the Mn valence state and oxygen vacancy concentration were changed by doping at Ca-site, while the total number of Mn ions remained intact. Ba, Sr, La, Sm, and Ce were the doping ions employed. Analyses revealed that the microwave absorption performance of CMO was linked to the Mn valence state and oxygen vacancy concentration. The Sr-CMO with the optimal microwave attenuation capability had the most Mn3+ ions and its dielectric loss is primarily due to polarization relaxation loss. In the microwave attenuation mechanism of La-CMO, which had the least oxygen vacancy content, conductive loss played a larger role. Through the double exchange interaction of Mn, the synergistic impact altered the microwave absorption performance. Hence, we can manipulate Mn valence state and oxygen vacancy concentration to improve the microwave absorption performance of CaMnO3, and the technique might be applied to other Mn-based absorbents.