In this paper, we discuss the principle of ecosystem complexity, and propose a method for evaluating the health of typical coral reef ecosystems in the South China Sea-"Organization and System Function Evaluation." The evaluation framework of this method includes four modules: the structure and function of coral reef ecosystems, the relationship between coral reef ecosystems and other marine ecosystems, the relationship with human social ecosystems, and the development constraints of coral reef ecosystems. The evaluation index system is divided into six levels, including target level, criterion level, factor level, and element level, totaling 67 indicators. We systematically put forward the process of coral reef ecosystem health evaluation, which improves the standardization and timeliness of coral reef health evaluation. The organizing power and system function evaluation method was used to evaluate the health of the coral reef ecosystem of the Paracel Islands from 2011 to 2018. The results show that the health index has fallen by 2.3%-2.4% annually since 2011. Except for a slight rebound in 2012 and 2015, the health index has shown a downward trend in the rest of the years. The overall evaluation is that the coral reef ecosystem of the Paracel Islands is sub-healthy. This result is consistent with the results of field investigations and questionnaire surveys on residents' lives around the Qilianyu Islands. We find that the development of fisheries in 2006-2008, the flooding of starfish in 2012, and the construction of islands and reefs in 2014-2015 had great impacts on the coral reef ecosystem. The fishery output dropped by 50%-80% in 10 years, which is also consistent with the evaluation results. It verifies the science and feasibility of the evaluation method from another angle.