Abstract: In view of the existing problems in sediment quality evaluation in China, based on the conventional monitoring indicators of coastal sediments in China and the standard of Marine Sediment Quality, the PCA was used to construct the evaluation index system and mathematical model of sediment quality. And the quantitative interval values of the three types of sediment quality comprehensive index F were divided. Then, the model was used in Jiulong Estuary and adjacent waters. The results showed that the sediment quality of Jiulong Estuary was mainly of class II assessed by the Marine Sediment Quality and characteristied by the pollution of both non point source and point source and its key area was in the coastal waters of Zhangzhou. The results of single factor evaluation indicated that the main pollution indexes were Zn, Cu and Pb. The evaluation results reflect well the current situation of sediment quality and provide technical support for protection and management in Jiulong Estuary.