A long-term experiment was conducted to investigate how long-term fertilization and rice straw incorporation into soil affect soil glomalin, C and N. The combined application of chemical fertilizer and straw resulted in a significant increase in both soil easily extractable glomalin (EEG) and total glomalin (TG) concentrations, as compared with application of only chemical fertilizer or no fertilizer application. The EEG and TG concentrations of the NPKS (nitrogen, phosphorus, and potassium fertilizer application + rice straw return) plot were 4.68% and 5.67% higher than those of the CK (unfertilized control) plot, and 9.87% and 6.23% higher than those of the NPK (nitrogen, phosphorus, and potassium fertilizer applied annually) plot, respectively. Application of only chemical fertilizer did not cause a statistically significant change of soil glomalin compared with no fertilizer application. The changes of soil organic C (SOC) and total N (TN) contents demonstrated a similar trend to soil glomalin in these plots. The SOC and TN contents of NPKS plot were 15.01% and 9.18% higher than those of the CK plot, and 8.85% and 14.76% higher than those of the NPK plot, respectively. Rice straw return also enhanced the contents of microbial biomass C (MBC) and microbial biomass N (MBN) in the NPKS plot by 7.76% for MBC and 31.42% for MBN compared with the CK plot, and 12.66% for MBC and 15.07% for MBN compared with the NPK plots, respectively. Application of only chemical fertilizer, however, increased MBN concentration, but decreased MBC concentration in soil.