It remains unclear whether biochar amendment can mediate changes in soil microbial communities caused by organic contaminants in the rhizosphere. This study demonstrated that phenanthrene stress resulted in significant shifts of both soil bacterial and fungal community structures, with the main changes of the relatively low-abundance microbial taxa. The microbial community response to biochar and/or oxalic acid (OA) differed under heavy phenanthrene stress. Biochar and/or OA led to the survival of certain microbial taxa that were inhibited by phenanthrene stress; therefore, microbial community structures were positively modulated. Many functional genes participating in polycyclic aromatic hydrocarbon (PAH) degradation were positively stimulated by heavy phenanthrene stress and further by OA addition or simultaneous application of biochar and OA. Biochar amendment and/or oxalic acid can positively mediate the shifts in soil microbial communities stressed by PAH, and tandem biochar-rhizoremediation may be an effective strategy for remediating PAH-contaminated soils.