A field experiment was conducted to study the remediation of agricultural soils polluted with polychlorinated biphenyls (PCBs) by several ecological controlling measures. After sequential stages of liming, plowing, planting alfalfa and paddy, a significant part of PCBs was removed from the soil, with an average removal rate of 86.9%. The treatment also decreased the toxic equivalency of dioxin-like PCBs in soil. Analysis of PCB congener composition showed that at stages of liming, plowing and alfalfa planting, the low-chlorinated biphenyls were removed; whereas at the stage of paddy planting, the high-chlorinated biphenyls were degraded. The ecological controlling measures had little influence on the microbial communities in soil. The results suggest that ecological control techniques could be widely applied in the remediation of agricultural soils with PCBs contamination.