ABSTRACT Long-term excessive application of inorganic fertilizers not only wastes resources but also contaminates the environment. The use of natural substitutes could overcome these drawbacks. We hypothesize that organic fertilizers could increase soil C, N sequestration and improve soil fertility more effectively than inorganic fertilizers, and that in particular effective microorganism (EM) could improve the effects of traditional compost. So, a long-term field experiment regarding improvement of soil fertility, protecting soil environment, and increasing of maize and wheat yield was conducted at China Agricultural University’s Qu-Zhou experiment station since 1993. Field experiment included EM compost treatment, traditional compost treatment, chemical fertilizer treatment, and unfertilized treatment. Soil organic C (SOC), total N, nutrient concentrations, pH, bulk density, and crop yields were determined. The results revealed that long-term repeated application of EM compost promoted soil C and N sequestration, increased soil nutrient contents, decreased soil pH and bulk density, enhanced crop yields in contrast to chemical fertilizer and control treatment. Soil organic C stocks (0-20 cm) were increased by 87.32%, 81.51%, 33.05%, 25.20% and soil total N stocks were increased by 93.26%, 77.53%, 37.64%, 34.83% in contrast to initial values in EM compost, traditional compost, chemical fertilizer and control treatments, respectively. Moreover, maize grain yields in EM compost, traditional compost, and chemical fertilizer treatments were significantly increased by 163.49%, 128.34%, 62.36% compared with control treatment, respectively. The effect of increased soil C and N sequestration, improving soil fertility and enhanced crop yields in application of compost appending EM was better than alone application of compost.