More and more attentions were paid on the environmental pollutions of wastewater discharged from scale pig farms, and it could provide scientific bases for formulating reasonable pollution control measures to study the structural changes of organic matter composition in piggery wastewater. In the present study, a laboratory-scale incubation experiment was carried out with piggery wastewater collected from different scale pig farms, and a continuous sampling was conducted at a certain interval during the process of incubation experiment. The main purpose of this study was to elucidate the change of structural composition of dissolved organic matter (DOM) in piggery wastewater during the process of organic degradation. All dried and solid DOM samples were achieved using filtration and freeze-drying methods. Spectral analysis of all DOM samples was completed with the application of Fourier transform infrared (FTIR) spectrometer. Results of spectral analysis showed a similar DOM structural composition was observed in the wastewater derived from different scale pig farms, and was mainly comprised of lipids, proteins, fulvic acids, polysaccharides, and phenolic compounds. With the increase in the incubation days, the percent of functional groups, related to proteins, phenolic acids, and lipids, decreased gradually and kept stable eventually, while these functional groups, linked with fulvic acids and polysaccharides, showed a significant increase and leveled off at the end. Compared with primary samples, fulvic acids and polysaccharides were the predominant fractions of DOM at 20 days after organic degradation, indicating a higher aromatic degree of DOM. Meanwhile, the degradation rate of OH bonded by intermolecular H-bond of cellulose was faster than OH bonded by intra-molecular H-bond of cellulose, whereas the latter was more sensitive to microbial degradation. The degradation rate of phenolic hydroxyl C—O was the fastest, followed by aromatic COOH, carbohydrate C—O, and amide CO.Furthermore, the carbohydrate C—O was apt to be utilized preferentially by microorganisms. In sum, the structural change of various DOM in piggery wastewater was different during the process of organic degradation.