Input of trace elements Fe and Zn in the lower reach of Liaohe Plain under different fertilization systems was studied by long-term field experiment and ICP-AES analysis. The results showed that Fe and Zn were mainly from organic manure in agro-ecosystem. The residual rate of organic manure through a feeding-composting cycle in the absence of bedding materials was 21.84%, which was lower than that of organic matter fertilized to soil after one year. The recycling rate of Zn through a feeding-composting cycle was 71.9%, and the recycling rate of Fe was 81.0%.