The limited number of studies on the ecotoxicological effects of perfluorinated compounds (PFASs) and their substitutes in soil requires the identification of a reliable diagnostic method, which constitutes the primary focus of this study. Previous investigations have demonstrated significant adverse effects on reproduction in small soil arthropods, specifically Folsomia candida, caused by PFASs. This study represents an initial exploration into the oxidative stress and reproduction-related gene expression induced by PFASs and their substitutes, aiming to clarify the molecular-level reproductive toxicity of PFASs. The findings reveal that three PFASs induce up-regulation in cytochrome P450 monooxygenase (CYP6N4V1, CYP6N3V2), genes associated with oxidative stress, with F-53B exhibiting the highest up-regulation amplitude (4.94 and 11.07 times respectively). Additionally, PFASs significantly suppress the activity of Cathepsin L (CTSL), a gene associated with reproduction. The expression of CTSL was observed to be only 64.2%, 39.0%, and 15% respectively compared to the control group levels when exposed to PFOA, PFBA, and F-53B treatments. These results indicate that perfluorinated compounds exert substantial regulatory effects on oxidative stress and reproductive related genes in Folsomia candida. Five differentially expressed genes - CYP6N3V2, CYP6N4V1, CTSL, VMO1, and Vitrec - can serve as target genes for early warning indicators regarding exposure to PFASs in soil-dwelling collembolan species such as Folsomia candida.