The toxicity of nanoparticles has attracted much attention, but the toxicity of nanoparticle types to soil fauna remains unclear. In this study, the earthworm (Eisenia fetida) was selected as a representative soil fauna to evaluate the toxicity of nano-hydroxyapatite (n-HAP), -zeolite (n-zeolite), and -iron tetroxide (n-Fe3O4) to soil fauna. The results showed that the skin ultrastructure, mortality, growth, antioxidant systems, and genetic material of the earthworms were affected to varying degrees by different nanoparticles. A filter paper test indicated that dermal exposure to nanoparticles primarily caused lesions in the cuticle, microvilli, and nucleus of the epithelial cells of earthworm skin. Soil incubation experiments showed that all types of nanoparticles could cause weight loss in earthworms, but only n-Fe3O4 resulted in their death. The reactive oxygen species and glutathione contents in earthworms exposed to n-Fe3O4 were much higher than those in earthworms exposed to n-HAP and n-zeolite. All nanoparticles stimulated the catalase and lactate dehydrogenase activity and damaged the DNA of earthworms. Integrated biomarker responses showed that the toxicity to earthworms increased in the following order: n-HAP < n-zeolite < n-Fe3O4. The characterization results indicated that the differences in surface hydroxyl groups and surface charge may be the cause of the differences in toxicity between n-HAP and n-zeolite with similar properties. The highest toxicity of n-Fe3O4 could be due to the size, spherical morphology, positive surface charge and the presence of Fe(II).