As an organic fertilizer, pig manure has long history of application in paddy fields and. it can increase soil organic carbon content, improve soil nutrient and increase crop yield. With the development of rural economics and the sharply increased demand for pig meat, intensive pig farms have become the main style of raising pigs and the resulting large amounts of pig manure have became a potential risk to the rural environment. The reuse of the pig manure was the inevitable choice to alleviate this environment risk. However, the plentiful application of feedstuffs with additives high in Cu and Zn bring a threat in the use of pig manure in agriculture. So, it is important to discover the accumulation dynamics and chemical characteristics of Cu, Zn and evaluate the carrying capacity of pig manure in paddy fields. The present study analyzed the total and available soil Cu and Zn content after different application times of pig manure in an organic fertilizer field experiment carried out from 1981. The treatments included combined green manure (22500 kg/hm²) and pig manure (22500 kg/hm²) in early rice (PM1), combined green manure (22500 kg/hm²) in early rice and pig manure (22500 kg/hm²) in later rice (PM2), combined green manure (22500 kg/hm²) in early rice and rice straw returning (4500 kg/hm²) in later rice (GMS), nitrogen- phosphorus- potassium fertilization (NPK). The results showed that long-term application of pig manure increased soil Cu and Zn content significantly, total Cu and Zn increased 7.69-9.52 mg/kg and 22.42-35.46 mg/kg after 30 year continuous application of pig manure, respectively. The proportion of available Cu and Zn content increased from 15% and 5% to 51% and 25% from 1981 to 2010. The pig manure application in early rice or later rice had no significant effect on the accumulation of soil Cu content, but it affected the accumulation of soil Zn significantly, the increase rate was much higher when the pig manures were applied in early rice than that of later rice. The available content of soil Cu, Zn increased more than 10 mg/kg from 2002 to 2010, which far higher than that accumulation in the former 22 years (1981 to 2002). This maybe the result of the higher content of Cu and Zn in the pig manure applied in this period and/or the saturation of soil stable state Cu and Zn. Based on the result of this study, the proper application amount of pig manure in red-soil paddy-fields is less than 9.5 t hm^-2 a^-1, which could maintain the soil Cu, Zn content below the national standard of second grade standard (pH<6.5) after 50 year continuous application of pig manure.