Soil microbial biomass content is usually regarded as an early indicator of changes in soil quality and soil fertility in paddy fields. Soil microbial biomass turnover is mainly influenced by the application of different fertilizer management systems. However, there is still a need to further investigate the effects of different long-term fertilizer management systems on soil microbial biomass turnover in paddy fields under the double-cropping rice (Oryza sativa L.) system. Therefore, the effects of different long-term (36 years) fertilizer practices on soil microbial biomass carbon (SMBC) and soil microbial biomass nitrogen (SMBN) contents, and the flux turnover rates of SMBC and SMBN at the 0–10 cm and 10–20 cm layers in a double-cropping rice field in southern China were investigated in the present paper. The field experiment included four different fertilizer treatments: MF, RF, OM, and CK. The results showed that SMBC and SMBN contents at the 0–10 cm and 10–20 cm soil layers with RF and OM treatments were increased compared with the MF and CK treatments. Compared with the CK treatment, SMBC contents at the 0–10 cm and 10–20 cm soil layers with RF and OM treatments increased by 35.72% and 50.28%, and 32.29% and 42.77%, respectively. SMBN contents at the 0–10 cm and 10–20 cm soil layers with RF and OM treatments increased by 15.52% and 22.70%, and 16.32% and 21.49%, respectively. The fluxes of SMBC and SMBN at the 0–10 cm and 10–20 cm soil layers with RF and OM treatments were significantly higher than those of the CK treatment. This result indicated that the flux turnover rates of SMBC and SMBN at the 0–10 cm and 10–20 cm soil layers with the MF, RF, and OM treatments were significantly higher than those of the CK treatment. Compared with the CK treatment, the flux turnover rates of SMBC and SMBN at the 0–10 cm and 10–20 cm soil layers with OM treatment increased by 46.10% and 48.59%, and 73.39% and 116.67%, respectively. SMBC and SMBN contents, and the flux turnover rates of SMBC and SMBN at the 0–10 cm layer were higher than those of the 10–20 cm layer under the same fertilizer treatment condition. Early rice and later rice yields with RF and OM treatments were significantly higher than those of the MF and CK treatments. As a result, the combined application of crop residue and organic manure with inorganic fertilizer management is a beneficial practice for increasing soil nutrients and rice yield under the double-cropping rice system in southern Chin.