Current ecosystem health assessments are mostly based on testing and analyzing the "vitality-organization-resilience" indexes of some breakpoint cases, which makes it hard to compare or integrate different research results across time and space. These results have narrow range of applications and do not conform to the disciplinary development trends of globalization and systematization. As the summation of the "vitality-organization-resilience" index system may ignore some important information, this article introduces a four-step diagnostic method of "interrogation-physical examination-laboratory tests-auxiliary examinations" to integrate an index system for the assessment of ecosystems. The method tests the ecosystem health using the entropy flow as measuring standard converted from substances or energy. It also analyzes related auxiliary indexes in different steps. Using energy and weight to calculate energy flow of an ecosystem, the diagnostic method can be divided into four main steps. First, unhealthy or important ecosystems are "inquired" based on investigators' academic sensitivity. Then the "physique" of ecosystems are characterized by the entropy value, followed by "laboratory" analyses of biological information (βi) and quality features (Ci). At last, "auxiliary examination" indexes are measured which provide series information related to vitality-structure of the ecosystems. The study showed that, by calculating the entropy flow and auxiliary indexes, various ecological systems can be distinguished into four dynamic states: unhealthy vitality type, unhealthy structure type, developing healthy type and mature healthy type. The data from three cited aquatic ecosystems, the South Lake, the Cedar Bog Lake and the Silver Spring, were used to analyze the strength of entropy flow, solar energy utilization rates, consumption and potential features of organization. The diagnostic results showed that the Silver Spring scored the highest and the Cedar Bog lake scored the lowest in "physique". Considering the environmental conditions and ecological efficiency, the Cedar Bog lake had the lowest consumption and the highest ordering potential in the three ecosystems. Both in the subtropical area, the South Lake's ordering potential equals only to that of the Silver Spring, a spring water river, which indicated that the lake has structural problems, and the Silver Spring was adapted to the river hydraulic state of high consumption and low potential. The results conformed with reality well. Some ecosystem concepts, like invasion and moderate interference, are difficult to describe quantitatively. The diagnostic method can also serve as a preliminary quantitative analysis in the subtle academic field. Measuring by ecological entropy flow, the phenomena of disturbance, plant diseases, insect pests and the invasion have similar essence although they have different performances. The diagnostics provided a preliminary quantitative analysis for ecosystem health in combination with its background and the changing factors.