Spatiotemporal distribution of total nitrogen (TN), total phosphorus (TP) in sediment of Dongting lake where the 500 hm2 freshwater pearl culture system is located in Summer and Winter from 2010—2011 was observed. The relationship between these TN and TP with chlorophyll-a in the water and the content changes of TN and TP under rice ecosystem were investigated. The results showed that the contents of TN and TP in sediment decreased from the South to the North. There was no significant seasonal change in TN. The highest content of TP appeared in Summer, which was 1.64 mg/g, and the lowest TP content was in Winter, which was 0.26 mg/g. The contents of TN and TP in sediment were positively correlated to chlorophyll a content. TN and TP contents in the sediment where rice ecosystem is accessible reduced 31.6% and 45.1%, respectively, compared to those in the sediment located in the central of the culture system where rice ecosystem is inaccessible. These results suggest that three-dimensional culture and rice cultivation in the ecosystem could balance the contents of TN and TP in the sediment.