Six strains of thermophilic high-efficient bacteria with amylase, lipase, protease and cellulase activity at 65 ℃ were isolated, purified and screened from food waste treatment system by using its thermostable and thermophilic characteristics and the basic principle of aerobiotic decomposition of organic compound. Pathogens, such as salmonellsa and shigella, were not found in security detection on the six strains, indicating the thermophilic bacteria isolated from pathogenic factors do not exist. With the disposing experiment of food waste，four thermophilic strains（HB1,HB2,HB4 and HB6）with high disposing efficiency for food waste were selected and produced for the thermophilic microbial agent. After being tested on the 100-kg disposing machine of food waste, the thermophilic microbial agent showed significant disposing efficiency on crude fat and crude fiber in food waste within 24 hours. When 5% thermophilic microbial agent was administrated at temperature up to 65 ℃, the degradation efficiency for crude fat and crude fiber was 30.7% and 11.3%, respectively. The crude protein content has increased 9.5%. The degradation efficiency was remained stable following a 48-hour test, demonstrating its rapid degradation ability on organic compound within 24 hours.