Long-term pig manure addition has been widely applied in red soil to improve soil fertility. However, the influence of combined utilization of pig manure and effective microbes (EM) on soil organic carbon (SOC) and Cd are not well understood. This study conducted a 23-year (1996–2019) long-term fertilization field trial to investigate the changes of different fractions of SOC and Cd under chemical fertilization (CF), pig manure (PM), and pig manure with effective microbes (PM + EM) treatments in an agricultural soil of Jiangxi Province, South China. The results showed that the pig manure addition significantly enhanced the contents of SOC and Cd in the soils compared with the CF treatments. Furthermore, with the increment of SOC, the PM + EM treatment significantly increased the contents of soil microbial biomass carbon, dissolved organic carbon and easily oxidizable carbon compared with the pig manure application alone. Meanwhile, compared with the CF treatments, the EM addition significantly enhanced the exchangeable and oxidizable fractions of Cd, thus the potential Cd environment risk due to pig manure application should be carefully assessed.