Inoculation with agrichemical-degrading endophytes can boost the metabolism of agrichemicals in rice. This beneficial microbe-plant interaction could prove useful for regulating fungicide residues in crop and for the remediation of contaminated farmland. However, the overall effects of introducing functional endophytes on rice rhizosphere microecology under fungicide exposure remain unclear, and the responses of rhizospheric organisms to degrading endophytes should be thoroughly investigated before further application of this symbiotic relationship. Therefore, in this study, we conducted pot experiments to investigate the stress responses of earthworms (Eisenia foetida), soil enzymes, and rhizospheric microorganisms in the rice rhizosphere under carbendazim (CBZ) exposure with and without inoculation with Stenotrophomonas pavanii DJL-M3, which is a CBZ-degrading endophyte. We applied the recommended dosage of CBZ, and then sampled rice rhizosphere soil at regular intervals; soil catalase, soil urease, and sucrose activity were detected immediately, whereas CBZ residue degradation was analyzed using high-performance liquid chromatography (HPLC). After 2 weeks of CBZ exposure, the earthworms were collected and their morphological characteristics were observed; we also detected earthworm malondialdehyde levels and superoxide dismutase and acetylcholine esterase activity in vivo to evaluate the degree of stress damage caused by CBZ contamination. The diversity index and carbon metabolic activity of rhizosphere soil microorganisms were analyzed using an Eco-Plate (Biolog, USA). Rice plants without CBZ treatment and microbial inoculation were used as a background control. The results showed that foliage spraying caused rhizosphere soil exposure with CBZ, which activated soil catalase, but inhibited soil urease and sucrose activity. The CBZ residue in rhizosphere soil led to oxidative damage in earthworms, as demonstrated by the accumulation of malondialdehyde and the overexpression of superoxide dismutase and acetylcholine esterase in vivo. The CBZ contamination significantly reduced the diversity and carbon metabolic activity of rhizosphere soil microorganisms. Within the 14-day experimental period, S. pavanii DJL-M3 inoculation boosted CBZ degradation in the rice rhizosphere by shortening the half-life of CBZ residue, thereby relieving fungicide stress on rhizosphere soil microorganisms and earthworms, as indicated by the enhanced carbon metabolic activity, Shannon index and McIntosh index of rice rhizosphere soil microorganisms, and the recovery of the earthworm survival rate to that of the unpolluted control. This stress relief ultimately significantly promoted soil urease and sucrose activity under CBZ exposure. Therefore, the degrading endophyte S. pavanii DJL-M3 could be used for the bioremediation of CBZ-contaminated paddy soil.