The high dependence on chemical fertilizers driven by crop yields has posed huge risks and challenges to soil quality and ecosystem balance for decades. The reduction and substitution of chemical fertilizers has now become a national strategy for high-quality agricultural development. The organic matter of livestock and poultry manure is converted into methane under highly anaerobic conditions, and the liquid by-products (biogas slurry) and solid residues (biogas residue) are also produced. The biogas slurry is rich in nitrogen, amino acids, and various mineral nutrient elements, being an efficient alternative to chemical fertilizers. Previous studies on the application of biogas slurry mainly focused on the effects of dosage and usage on crop yield and soil properties. The impact on soil fauna communities was insufficient yet. Soil arthropods participate in soil biochemical cycles, stimulating the metabolism of fungi and bacteria and maintaining the balance of the soil ecosystem. Due to their sensitive response to habitat changes, soil arthropods are used as important indicators to reflect soil health and stability. However, there is no investigation on the changes of soil arthropod communities under the condition of biogas slurry instead of chemical fertilizers. In the present study, the effects of different dosage of biogas slurry (0, 100, 200, and 300 m³/hm²) and substitution of biogas slurry (0%, 33%, 66%, and 100%) to chemical fertilizers on soil small- and medium-sized arthropod communities were investigated in coastal reclaimed wheat fields with repeated application of biogas slurry for 5 years in Dongtai city, Jiangsu, China. The results showed that the predominant soil fauna groups in wheat field were Prostigmata, Oribatida and Collembola, accounting for 52.09%-53.33%, 22.42%-23.86% and 13.14%-16.51% of the total catches, respectively. When the amount of biogas slurry increased from 0 to 300 m³/hm², the density of soil fauna increased by 94%, the number of groups increased by about 2, and the dominance index increased by 9.4% (P < 0.05). The density of soil fauna, number of groups and dominance index arrived the highest when using 66% of biogas slurry to replace chemical fertilizers. Therefore, the application of biogas slurry could significantly increase the density, group number, and dominance index of small- and medium-sized arthropods in the soil. When the ratio of biogas slurry to replace chemical fertilizer was 66%, the promotion effect was the best. In addition, principal component analysis showed that Collembola, Prostigmata and Oribatida were much sensitive to biogas slurry application alone or biogas slurry in place of chemical fertilizers. They could be used as indicators of the response of soil small- and medium-sized arthropods to fertilization.