The electromagnetic compatibility (EMC) problem caused by large-scale air-core reactors in substation is increasingly serious. The measured maximum interference of 110 V DC system in a substation has amounted to 52 V, which seriously affects the safe and stable operation of substations. In order to research the interference characteristics, the interference’ s amplitude, frequency, distribution characteristic are measured, and three-dimensional scale models of the reactor, ground network, and DC system are established and their equivalence is verified. On this basis, this paper presents the ways to improving the height of the reactor and laying shielding material under the reactor, and evaluates the measures’ effects. From the simulation results, the common-mode interference voltage gives priority to three harmonics. The anti-interference method proposed can effectively reduce the influence of air-core reactor on DC system.