The ecological footprint method put forward and improved by William Rees and Mathis Wackernagel presents a methodologically simple but integrated framework for national natural capital accounting, which is capable of measuring the impact of Human's consumption on ecosystem. Based on the ecological footprint theory and calculation method, a flow network analysis method was introduced to illuminate the structure of complex ecological economic system, and the relationship among ecological footprint, diversity and development capacity was analyzed. In this paper, the ecological footprints of China and its provinces was calculated and compared with the national and local ecological carrying capacity. The results showed that the ecological footprints of China and most of its provinces were beyond the available ecological capacity, and China and its most provinces run 'national or regional ecological deficit'. In case of China, the national ecological deficit was 0.645 hm2 per cap in 1999. Secondly, we introduced a flow network analysis method, taking various ecological productive area as note, and adopted Ulanowicz's development capacity formula to analyze the relationship among ecological footprint diversity, development capacity and output. The results demonstrated that Ulanowicz's development capacity was a good predictor of economic system output. At the same time, two distinct ways to change development capacity were produced. Increasing ecological footprint or increasing ecological footprint's diversity would both increase development capacity. Due to the fact that the ecological footprints had already been beyond bio-capacities, the only way to increase development capacity was to increase ecological footprint's diversity. The positive relationship between ecological footprint diversity and resources utilization efficiency demonstrated that there was no conflict between increasing ecological footprint's diversity and reducing footprints while not comprising our quality of life.