The purpose of this study was to investigate the protist community and soil microbial carbon metabolism with pig manure application in the dryland red soil of south China. The long-term field experiment was conducted in maize mono-cropping system at the National Agro-Ecosystem Observation and Research Station in Yingtan, Jiangxi Province. Four treatments included no manure (M0), low manure (M1), high manure (M2), and high manure with lime addition (M3). The high-throughput sequencing of 18S rRNA gene was used to explore the diversity and structure of soil protist community, and to estimate the effect of protists-microorganisms interaction on microbial carbon metabolism and maize yield. Our results showed that soil chemical properties significantly varied under the four fertilization treatments. Soil pH, soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP), available phosphorus (AP), and available potassium (AK) were significantly increased under manure treatments. Compared with M0 treatment, manure treatments (M1, M2, and M3) significantly enhanced the biomass and diversity of protist, and remarkably modified the protist community structure. The protist community composition was mainly affected by soil TP, pH, AP, TN, SOM, and AK. Manure application significantly improved the bacterial and fungal biomasses, and consequently promoted microbial carbon metabolism indicated by the values of average well color development (AWCD). Structural equation modelling indicated that soil pH and AP could indirectly increase microbial carbon metabolism and maize yield through regulating the diversity and structure of protist community. Taken together, we provide the scientific basis for promoting the microbial diversity in the dryland red soil, and maintaining soil health and ecosystem service functioning.