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The use of carbon nanoparticles (CNPs) as a fertilizer synergist to enhance crop growth has attracted increasing interest. However, current understanding about plant growth and soil response to CNPs is limited. In the present study, we investigated the effects of CNPs at different application rates on soil properties, the plant growth and nutrient use efficiency (NUE) of corn (Zea mays L.) in two agricultural soils (Spodosol and Alfisol). The results showed that CNPs affected corn growth in a dose-dependent manner, augmenting and retarding growth at low and at high concentrations, respectively. The amendment at the optimal rate of 200 mg CNPs kg−1 significantly enhanced corn growth as indicated by improved plant height, biomass yield, nutrient uptake and nutrient use efficiency, which could be explained by the higher availability of phosphorus and nitrogen in the amended soils. The application of CNPs largely stimulated soil urease activity irrespectively of soil types. However, the responses of dehydrogenase and phosphatase to CNPs were dose dependent; their activity significantly increased with the increasing application rates of CNPs up to 200 mg kg−1 but declined at higher rates (>400 mg kg−1). These findings have important implications in the field application of CNPs for enhancing nutrient use efficiency and crop production in tropical/subtropical regions.