Chloramphenicol (CAP) has long been used extensively in agriculture and is severely toxic to the biological environment. Microwave catalysis appears a promising method for soil remediation due to its fast and effective heat transfer, but it is challenging to prepare catalysts with good electromagnetic wave absorption and robust catalytic activity. In this study, atomically dispersed Fe on three‐dimensional N‐doped carbon supports (3D Fe‐NC) is firstly used for microwave remediation of soil. Thanks to the synergistic effect of microwave “hot spots” and reactive oxygen species (•OH, •O2−), 3D Fe‐NC can completely remove 99.9% of CAP in 5 min. The removal rate constant is nearly twice that of commercial activated carbon. Significantly, the germination rate of lettuce seeds in microwave‐repaired soil contaminated by CAP reaches 70%. This work demonstrates the application of Fe single‐atom catalyst in microwave remediation of contaminated soil, providing a novel insight for agricultural soil remediation.