To investigate the effect of arbuscular mycorrhizal fungal (AMF) hyphae on remediation of polychlorinated biphenyls (PCBs) contaminated soils and its related mechanisms, an illumination incubation experiment was conducted by using the rhizobox system to separate plant root and AMF hyphae. The experiment included a treatment inoculated with Glomus mosseae and a non-mycorrhizal control, using Cucurbita pepo L. as test plant. The soil in hyphal compartment was separated into 4 horizontal layers, which were used for PCBs and phospholipid fatty acid (PLFA) analysis. The results indicated that AMF hyphae could penetrate the nylon mesh and the hyphal length decreased with the increased distance from nylon mesh. PCBs dissipation rates in different soil layers of the AMF inoculated treatment ranged from 35.67%–57.39%, and were significantly higher than that in the control (17.31%, P<0.05). Soil Tri-, Tetra-chlorinated biphenyls and total PCBs concentrations were found significantly and negatively correlated with soil hyphal length (P<0.01). Soil microbial PLFA biomass, especially bacterial biomass, negatively correlated with soil tri-chlorinated biphenyls contents significantly (P<0.05). This study suggested that the AMF hyphae can promote the remediation of PCBs contaminated soil by increasing microbial biomass and by altering microbial community composition in the hyphosphere soil.