The coral reef ecosystem is an ecosystem with high biodiversity and high resource productivity. The ecosystems have important ecological effects, biogeographic functions and socioeconomic benefits. However, coral reef ecosystems are extremely fragile, and global climate change and increasing human activity have led to serious damage and degradation of coral reef ecosystems worldwide. The increase in nutrient concentration caused by anthropogenic activities is also considered as an important reason for the degradation of coral reef ecosystems in some areas. Therefore, it is extremely important to research the relationship between nutrient concentration and coral reef ecosystem decline and investigate nutrient distribution in coral reef area. In order to investigate the effects of surface seawater nutrient distribution on coral reef ecosystem in the coral reef sea area of Luhuitou, Sanya, this study arranged sampling section in the coral reef area and collected surface water samples, then investigated the concentration level of nitrite (NO2-N), nitrate (NO3-N), ammonium (NH4-N), soluble reactive phosphorus (SRP), silicate (SiO3), chlorophyll a (chl a), dissolved Oxygen (DO), etc. in the summers from 2014-2016. The results showed that the average concentrations of Dissolved inorganic nitrogen (DIN) of the three years were 2.941, 1.766, 23.428 μmol/L, those of SRP were 0.493, 0.419, 0.143 μmol/L, those of CHL were 2.304, 1.90, 1.251 mg/m3, and those of SiO3 were 10.275 (2015), 8.506 μmol/L (2016), respectively. The survey was made from 2014 to 2016, the overall concentration of nutrients in summer was higher. The general trend is that the summer nutrients in this area are higher than those in the past 20 years, it may be related to an increase in human activity. In all indicators, the increase trend of DIN is the most significant. N/P showed an upward trend and it means that nitrogen pollution is increasing. Possible causes are mainly from the pollutants emitted during the production process of terrestrial industry and agriculture. The higher nutrient input and the increase of N/P may cause the phosphorus limit of the nutrient, leading to the change of the community structure of the coral reef ecosystem. The change of the community structure will have a negative impact on the stability of the coral reef ecosystem. At the same time, as compared with other coral reefs in the world, the level of nutrient concentration in the reef area of Luhuitou in Sanya is similar to that in Daya Bay of Shenzhen, which is the same as that in Chinese coastal coral reefs. The level of nutrient concentration in the reef area of Luhuitou in Sanya is far higher than that in Zhubi reef area of the Nansha Islands in the South China Sea, and higher than that in other coral reef areas of the world, that means that the shore reef sea area is influenced by a serious land-based nutrients input. Higher levels of nutrients may cause local eutrophication, followed by red tides, have a greater threat to the normal development of coral reefs, and will cause serious degradation of the coral reef ecosystem. Therefore, the increase of nutrient, especially nitrogen, is probably one of the factors that would lead to the degradation of coral reef ecosystem in recent years in the reef area of Luhuitou.