Swine wastewater (SW) poses a great threat to the environment due to its high-nutrient pro les if not properly managed. Advanced biological treatment method is an e cient method to treat SW by screening potent microalgae or bacterial strains. In this study, activated sludge, nine locally isolated heterotrophic nitri cation bacteria and one microalgal strain (Chlorella) were used as inoculums in treating a local SW.Their treatment e ciencies were compared, while the nitrogen removal mechanisms and microbiome pro le were explored in detail. It was found that certain heterotrophic nitri cation strains had a slight advantage in removing chemical oxygen demand and phosphorus from SW, with the highest removal e ciencies of 83.9% and 76.2%, respectively. The removal e ciencies of ammonia nitrogen and total nitrogen in wastewater by microalgae reached 80.9% and 66.0% respectively, which were far higher than all the heterotrophic nitri cation strains. Biological assimilation was the main pathway of nitrogen conversion by microalgae and heterotrophic nitrifying bacteria; especially microalgae showed excellent biological assimilation performance. Correlation analysis showed that Comamonas was highly positively correlated with nitrogen assimilation, while Acidovorax was closely correlated with simultaneous nitri cation and denitri cation. This study gives a comparison of microalgae and heterotrophic nitrifying bacteria on the nitrogen transfer and transformation pathways.