To enhance the electromagnetic protection and microwave absorption properties of concrete structures, magnetite aggregates (MAs) were used to prepare magnetite concrete (MC). By measuring electromagnetic parameters and microwave reflection loss (R_loss), the electromagnetic absorbing properties of the MC was analyzed, and its microstructures were characterized. By establishing the structure-activity relationship between electromagnetic properties, microwave absorption properties and microstructures, the enhancement mechanism of MAs on the absorbing efficiency of MC was revealed. The results showed that MAs effectively enhance the electromagnetic loss ability and impedance matching characteristics of MC by improving its dielectric and magnetic properties, as well as influencing its pore distribution and C-S-H gel structures. Compared with the control group, the mean R_loss of the concrete with 100 % MAs content reduced to -7.68 dB, and the effective bandwidth expanded to 7.21 GHz, enabling it absorbing microwave efficiency to be more than 80 % at wide frequency range.