Phytoremediation with biochar addition might alleviate pollutant toxicity to soil microorganism. It is uncertain to what extent biochar addition rate could affect activities of enzymes related to soil nitrogen (N) mineralization and alter fungal community under the phytoremediation. This study aimed to reveal the effects of Medicago sativa L. (alfalfa) phytoremediation, alone or with biochar additions, on soil protease and chitinase and fungal community and link the responses of microbial parameters with biochar addition rates. The alfalfa phytoremediation enhanced soil protease activities, and relative to the phytoremediation alone, biochar additions had inconsistent impacts on the corresponding functional gene abundances. Compared with the blank control, alfalfa phytoremediation, alone or with biochar additions, increased fungal biomass and community richness estimators. Moreover, relative to the phytoremediation alone, the relative abundances of phylum Zygomycota were also increased by biochar additions. The whole soil fungal community was not significantly changed by the alfalfa phytoremediation alone, but was indeed changed by alfalfa phytoremediation with 3.0% (w/w) or 6.0% biochar addition. This study suggested that alfalfa phytoremediation could enhance N mineralization enzyme activities and that biochar addition rates affected the responses of fungal community to the alfalfa phytoremediation.