The Closed Ecology Experiment Facilities (CEEF) were installed to collect data for estimation of transfer of radionuclides from atmosphere to humans in the ecosystem. The first target among the radio-nuclides is 14C. In order to validate function of material circulation in an experimental system constructed in the CEEF, circulation of air constituents, water and materials in waste was demonstrated connecting the Closed Plant Experiment Facility (CPEF) and the Closed Animal and Human habitation Experiment Facility (CAHEF) of the CEEF, since 2005 to 2007. The CPEF has a Plant Cultivation Module (PCM), which comprises of three plant chambers illuminated solely by artificial lighting, one plant chamber illuminated by both natural and artificial lighting, a space for preparation, and an airlock, and a physical/chemical material circulation system. The CAHEF has an Animal keeping and Human habitation Module (AHM), which is comprised of an animal room, a habitation room, a closed corridor, an airlock, and a physical/chemical material circulation system. During the material circulation experiments, two humans (called eco-nauts) stayed in the CEEF being isolated from the outside. In these experiments, 23 crops including rice, soybean, peanut, and sugar beet were cultivated in the PCM, and two goats stayed in the AHM. Almost all of the food consumed by the eco-nauts and the feed to the goats (straw, leaf and bran of rice, leaf and stem of soybean, and leaf, stem and shell of peanut) were produced from crops in the PCM. The oxygen added to the air in the PCM by photosynthesis of crops was separated and supplied to the air in the AHM. Increased carbon dioxide in the AHM atmosphere by respiration of eco-nauts and goats was separated and supplied back to the air in the PCM. In addition to food production and circulation of air, water circulation was also conducted in the CEEF in 2006 and 2007. In addition to them, waste processing and circulation of materials from the waste in the CEEF were also conducted in 2007. Closed habitation experiments in 2005, each lasting one week, were conducted three times. In 2006, although the eco-nauts changed by week, 2-week habitation was conducted three times. In 2007, 1-week, 2-week (two times) and 4week habitation were conducted. Data obtained in all of above experiments conducted in 2005–2007 will be also invaluable for examination and planning of human-in-loop systems necessary for independent long-term human living habitats such as lunar or Martian base.