Anaerobically digested swine wastewater (ASW) purification by microalgae provides a promising strategy for nutrients recovery, biomass production and CO2 capture. However, the characteristics of ASW from different cleaning processes vary greatly. At present, the cultivation of microalgae in ASW from different manure cleaning processes is rarely investigated and compared. That may bring uncertainty for microalgae growth using different ASW in large-scale application. Thus, the ASW from three cleaning processes were tested for cultivating microalgae, including manure dry collection (I), water flushing (II) and water submerging processes (III). The characteristics of ASW from three manure cleaning processes varied greatly such as nutrient and heavy metals levels. High concentration of ammonia and copper in ASW significantly inhibited microalgae growth. Fortunately, the supply of high CO2 (10%) effectively alleviated negative influences, ensuring microalgal growth at low dilution ratio. The characteristics of three ASW resulted in significant differences in microalgae growth and biomass components. The maximal biomass production in optimal diluted ASW-I, II and III reached 1.46 g L−1, 2.19 g L−1 and 2.47 g L−1, respectively. The removal of organic compounds, ammonia and phosphorus by optimal microalgae growth in diluted ASW-I, II and III was 50.6%/94.2%/64.7%, 63.7%/82.3%/57.6% and 83.2%/91.7%/59.7%, respectively.The culture in diluted ASW-I, II and III obtained the highest lipids production of 12.1 mg L−1·d−1, 16.5 mg L−1·d−1 and 19.4 mg L−1·d−1, respectively. The analysis of lipids compositions revealed that the proportion of saturated fatty acids accounted for 36.4%, 32.4% and 27.9 % in optimal diluted ASW-I, II and III, as ideal raw materials for biodiesel production.