The root-knot nematode (Meloidogyne spp.) is one of the major challenges in eggplant (Solanum melongena L.) production. Fluopyram, known to be an effective fungicide, is also used for controlling root-knot nematode. However, in China, little information is currently available regarding the efficacy of fluopyram via chemigation against root-knot nematode and its effects on soil properties. For this, the objective of this work was to test mortality of root-knot nematode, functional diversity of soil microbial community, activity of soil enzyme after fluopyram applicated by chemigation. The results of two field experiments revealed that concentration of 60 g·ha-1 fluopyram applied with 200 L·ha-1 irrigation water at 2 L·h-1 flow velocity was the most effective chemigation parameters for controlling eggplant against root-knot nematode. The functional diversity of the soil microbial community was significantly affected by fluopyram. The activities of soil urease and β-glucosidase decreased during the initial stages but recovered at later stages. In brief, fluopyram has advantageous for the efficient control of root-knot nematode with no deleterious effects on soil properties as well as chemigation is positive for application in karst landscape in Guangxi.