Swine wastewater contains a high concentration of ammonia nitrogen (NH4+-N), chemical oxygen demand (COD), suspended solids, phosphorus, and other nutritional substances. The two-stage anoxic/oxic (A/O/A/O) process can effectively solve the removal problem of high concentration ammonia nitrogen, so it has great potential in the treatment of swine wastewater. However, the effluent COD in the A/O/A/O process is relatively high, and difficult to meet the discharge standard. This part of COD results from refractory organic matters, it is necessary to investigate dissolved organic matter (DOM) components and their changes in wastewater treatment. Fluorescence excitation-emission matrix (EEM) is a new spectral fingerprint analysis technology and Parallel Factor (PARAFAC) analysis is an effective method to decompose fluorescence EEM into independent components. In this paper, the swine wastewater was treated by a step feed A/O/A/O process. The influent COD fluctuated greatly in the range of 3104~6210 mg/L. whereas the effluent COD was significantly degraded and remained at about 500mg/L. The average removal rate of COD was 89%. The influent NH4+-N ranged from 1043 mg/L to 1361 mg/L, whereas the effluent NH4+-N remained at about 35 mg/L. The average removal rate of NH4+-N was 97%. By the EEM-PARAFAC analysis, the fluorescence signal of influent and effluent samples could be both divided into four kinds of DOM components. The influent DOM was mainly composed of C1, C2, and C3, and the effluent DOM was divided into C2, C3, and C4. The C1 and C2 components in the influent water were nearly degraded in the effluent. The fluorescence intensity of C3 in influent and effluent samples was nearly unchanged. The newly generated C4 component in the effluent was almost absent in the influent. It indicates that C4 was a microbial metabolic byproduct.