The size reduction of atomic clocks is a long-standing research issue. Many atomic clocks such as passive hydro-gen masers (PHMs) and compact rubidium masers (CRMs) use iris-loaded resonance cavities (IRCs) as their microwave cavities because they can dramatically reduce the radical sizes of the atomic clocks. In this paper, the electromagnetic characteristic of the IRC is investigated by a theoretical model based on electromagnetic field theory. The formulas to cal-culate the resonance frequency, quality factor, and magnetic energy filling factor are presented. The relationship between the IRC structure and its electromagnetic characteristic is clarified. The theoretical calculation results accord well with the electromagnetic software simulations and experimental results. The results in this paper should be helpful in understanding the physical mechanism of the IRC and designing the atomic clocks.