Abstract: There is a large amount of pill residues with high water content resulting in serious environment pollution in citrus processing for juice. Efficiently reducing pollution is thus very urgent. In the present experiment, citrus pill residues was mixed with ground wheat straws in various proportions and inoculated with thermal bacteria (Bacillus sp) decomposing pectin and cellulose. The main object is to develop a technique to treat citrus pill residues for organic fertilizer production and decontamination by high temperature compost and to test the effect of organic fertilizer by applying in flue-cured tobacco. It was found that the microbial groups and numbers were highest in compost at the beginning. They were lowest and only two group of bacteria, being identified as the inoculated thermophilic Bacillus sp decomposing pectin and cellulose, in high temperature period. The microbial groups increased again thereafter, but the numbers changed little or slightly increased in final stage as compared to high temperature period. In composting process, temperature raised quickly to 60-73℃ and then decreased, which followed by constant linear reduction of water content. Nutrient contents in compost materials increased quickly (nitrogen) and constantly (phosphorus and potassium), and then nitrogen decreased slowly after reaching to the highest. pH value changed similarly as nitrogen, ranged from 4.04 to 4.94 in compost. During the fermentation, the color of citrus pill residues changed from yellow into light gray, dark gray or black. After 40 days fermentation with inoculation of thermophilic Bacillus sp decomposing pectin and cellulose, the compost materials fitted the national standard of organic fertilizer (NY525-2002). Water content decreased from 82.2% to 20.2%. The total nutrient (N+P2O5+K2O) reached to 4.57% and organic matter was as high as 66.5% in compost materials. The citrus pill residues changed into dark gray or black at the end of fermentation. Rational combination fertilization of 50% chemical fertilizer and 50% organic fertilizer produced from citrus pill residues could increase significantly the yields and improve the qualities of flue-cured tobacco in fertilizer efficiency test.