Fluoxastrobin (FLUO), one of the best-selling strobilurin fungicides, could prevent fungal diseases from oilseed crops, fruits, grains, and vegetables. The widespread use of FLUO leads to the continuous accumulation of FLUO in soil. Our previous studies have demonstrated that FLUO exhibited different toxicity in artificial soil and three natural soils (fluvo-aquic soils, black soils, and red clay). The toxicity of FLUO was greater in natural soil than the artificial soil, specifically, showed the highest toxicity in fluvo-aquic soils. To better investigate the mechanism of FLUO toxicity to earthworms (Eisenia fetida), we selected fluvo-aquic soils as representative soil and used transcriptomics to study the gene expression in earthworms after FLUO exposure. The results demonstrated that the differentially expressed genes in earthworms after FLUO exposure mainly presented in pathways involving protein folding, immunity, signal transduction, and cell growth. It may be the reason why FLUO exposure stressed the earthworms and affected their normal growth activities. The present study fills gaps in the literature regarding the soil bio-toxicity of strobilurin fungicides. It also sounds the alarm for the application of such fungicides even at the low concentration (0.1 mg kg−1).