Based on the long-term experiment in Taoyuan Agroecosystem Experimental Station of Chinese Academy of Sciences, this paper studied effects of long-term quantitative fertilization on accumulation and availability of Cd, Pb, Cu and Zn in the red paddy ecosystem. The application of chemical fertilizers decreased the concentration of Cd in soil, and Cd uptake by rice might be the main reason for this. When recycling of organic matter brought some nutrient elements back into the soil, Cd was among them. The effect of the recycling changing soil properties and hence soil Cd played a more important role than the effect of Cd uptake by rice in accumulation of Cd in the soil. Both application of chemical fertilizers and recycling of organic matter increased Pb in the red paddy soil, but did not have any significant effect on Cu and Zn. Long-term application of chemical fertilizers had little effect on Cd, Pb, Cu and Zn, while recycling of organic matter improved availabilities of Cd and Zn significantly. The increase in soil organic matter and the decrease in soil pH caused by recycling of organic matter might be the main reason for the promotion of availabilities of Cd and Zn.