To learn the carbon metabolism of microbial communities of moving bed biofilm reactor which was adjusted to different process in recirculating aquaculture systems, and find out if microorganism had a better nitrification in moving bed biofilm reactor under the condition of energy conservation. Experiments changed the moving bed biofilm reactor to different process which were O²、A/O and O/A, respectively.Then, using Biolog-ECO method to analyse the characteristics of microorganism on the carbon source metabolism of moving bed biofilm reactor. The results showed that, the second section of O² process was the best of AWCD of microbial communities cultured in different process, then was the first section of A/O process, and the first section of O/A process was the worst.The utilization degree of carbon sources of microbial communities in different process show preference to amino acids and amines, the second section of O² process and the first section of A/O process were higher than the other process.The first section of O/A process was the highest in micro-organism diversity indices, then were the second section of O² process and the second section of O/A process, and the first section of O² process was the lowest.The PCA(principal component analysis) showed that contribution of PC1 of the micro-organisms in different process was 32.89%, PC2 was 25.91%, and there were 16 types of substrates in PC1 over 0.5 of load, and 14 in PC2.L-Asparagine and L-Arginine of amino acids, N-Acetyl-D-Glucosamine of carbohydrates, Tween 40 and Tween 80 of polymers, 4-Hydroxy Benzoic Acid of phenolic acids and Phenylethylamine of amines were better utilized by micro-organisms.γ-Hydroxybutyric Acid of carboxylic acids, D, L-α-Glycerol Phosphate of carbohydrates and 2-Hydroxy Benzoic Acid of phenolic acids were utilized worse.This experiment through changing the work conditions of moving bed biofilm reactor to study its carbon metabolism of microbial communities, which can provide a basis for further study of recirculating aquaculture system.