Climate warming, variation of East Asian atmospheric system have affected the Chinese offshore environment through the air-sea interaction, the coastal waters of South China Sea had been influenced, leading a corresponding impact on the coral reef growth. This paper reports on coral coverage and dominant coral species changes in Xu wen National Coral Reef Nature Reserve, examines their relationship with meteorological factors anomalies recorded by satellite. The study reveals that: compared to the period from 1979 to 2003, the temperature of surface coastal water dropped significantly in South China Sea in 2004-2008, the divergence of low layer of atmosphere over it strengthened, produced a zonal westerly anomaly field, which had an opposite direction to the local northeastern trade wind. The increasing of suspended matter in water, the decreasing of down welling in northwestern South China Sea, made the water quality deteriorating, water transparency decreased significantly, coral reef survival environment worsened, which would cause adverse effects on coral reef building capacity in the Reserve. Continued monitoring efforts are necessary to further assess the relationship between coral building capacity and in situ meteorological factors anomalies and improve the use of the dataset in future regional degradation predictions.