Abstract: To evaluate the effects of biogas residues derived from different manure sources and their compost products on soil health and soil food webs when applied to farmland, this study selected soil nematodes as indicator organisms and conducted a pot experiment. Four fertilization treatments were established: chicken manure biogas residue (FB), cattle manure biogas residue (CB), compost from chicken manure biogas residue (FC), and compost from cattle manure biogas residue (CC), with no fertilization set as the control (CK). The responses of soil nematode community structure, diversity, and ecological indices to manure source types and material categories were systematically analyzed. The results indicated that compared with the control, the application of both chicken manure and cattle manure biogas residues significantly increased the number of bacterivores. The average abundance of bacterivores in these two biogas residue treatments was 2.77 times that in the organic fertilizer treatments and 8.26 times that in the control, respectively. Additionally, the incorporation of biogas residues into soil was beneficial to omnivore-predators, with chicken manure biogas residue exhibiting the most prominent effect. Relative to other treatments, the average abundance and average relative abundance of omnivore-predators in the FB treatment increased by 83.0% and 68.0%, respectively. The nematode basal index, mature index 2–5, and faunal analysis revealed that soils treated with chicken manure biogas residue experienced less disturbance and possessed a more structured food web compared to soils under other treatments. Principal component analysis (PCA) demonstrated that biogas residues exerted a stronger influence on soil nematode communities than organic fertilizers, implying that the treatment of biogas residues through aerobic composting would attenuate their effects on the belowground ecosystem following field application. Overall, this study highlights the strong bottom-up regulatory effect of chicken manure biogas residue within soil food web, as well as its advantages in maintaining nematode diversity and improving soil health conditions.