Based on a long-term stationary experiment on problems in continuous monocropping of peanut from 1996 to 2008 in the Ecological Experimental Station of Red Soil, Chinese Academy of Sciences, effects of fertilization on plant growth, yield and incidence of soil-borne diseases of peanut were studied. Soil-borne disease occurred in all the fields under continuous monocropping in 2008, while the incidence was lower in Treatments M (organic manure), BM (organic manure + effective microorganisms) and BMT (organic manure + effective microorganisms + trace materials) than in Treatments F (chemical fertilizer) and TF (chemical fertilizer + trace materials) in the same year. No matter what fertilizer was applied, continuous monocropping decreased height, weight and yield of peanut, and the effect became more severe over time. Peanuts were obviously better in growth and yield in Treatments M, BM and BMT than in Treatments F and TF. Application of organic manure and effective microorganisms decreased the incidence of soil-borne diseases, deferred the declining trend of pod yield and improved plant growth, while the application of microelements did not have such effects. A significant negative correlation between pod yields and disease incidence indicated that soil-borne diseases is one of the main obstacles to continuous monocropping of peanut.