•Microalgae were cultured in aquaculture wastewater by newly developed MPBR.•Concentrated microalgae cultivation with diluted wastewater was achieved in MPBR.•MPBR could remove most of the nutrients with a short HRT of only 1 day.•Unionized ammonia was completely removed by microalgae cultivation in MPBR. An efficient continuous microalgae cultivation process for biomass production and nutrients removal from aquaculture wastewater was developed using a membrane photobioreactor (MPBR). Chlorella vulgaris and Scenedesmus obliquus were firstly batch cultured in aquaculture wastewater. C. vulgaris showed better performance with the specific growth rate of 0.17d−1 and was continuously cultivated in MPBR. The average volumetric biomass productivity in the MPBR operated at HRT of 1 day was 42.6mgL−1d−1, which was 5.8-fold larger than that achieved in batch cultivation in flask. Advanced nutrients removal from aquaculture wastewater was also achieved in MPBR. The average reduction in TN and TP was 86.1% and 82.7%, respectively, after stabilization. The corresponding effluent concentration was below 1.30 and 0.12mgL−1 for TN and TP, respectively. Unionized ammonia, which is usually toxic to aquatic animals, was also effectively removed in MPBR, with effluent concentration below 0.002mgL−1.