The widespread production and use of zinc oxide nanoparticles (ZnO-NPs) in recent years have posed potential threat to the ecosystem. This study aimed to investigate the ecotoxicological effect of ZnO-NPs on soil microorganisms using laboratory microcosm test. Respiration, ammonification, dehydrogenase (DH) activity, and fluorescent diacetate hydrolase (FDAH) activity were used as ecotoxicological parameters. The results showed that in the neutral soil treated with 1 mg ZnO-NPs per g soil (fresh, neutral), ammonification was significantly inhibited during the study period of three months, but the inhibition rate decreased over increasing time. Inhibition in respiration was observed in the first month of the test. In various ZnO-NPs treatments (1 mg, 5 mg, and 10 mg ZnO-NPs per g soil), DH activity and FDAH activity were inhibited during the study period of one month. For both enzyme activities, there were positive dose–response relationships between the concentration of ZnO-NPs and the inhibition rates, but the curves changed over time due to changes of ZnO-NPs toxicity. Soil type affected the toxicity of ZnO-NPs in soil. The toxicity was highest in the acid soil, followed by the neutral soil. The toxicity was relatively low in the alkaline soil. The toxicity was not accounted for by the Zn released from the ZnO-NPs. Direct interaction of ZnO-NPs with biologic targets might be one of the reasons. The adverse effect of ZnO-NPs on soil microorganisms in neutral and acid soils is worthy of attention.