The application of biological process for the high saline mariculture wastewater treatment was hindered primarily by salinity and settleability. Photogranule is an effective wastewater treatment technology with excellent settleability and resistance to environmental changes. In this study, internal circulating photogranular membrane bioreactor (IC-PMBR) and internal circulating photogranular sequencing batch bioreactor (IC-PSBR) were constructed to cultivated photogranules. The result showed that mature photogranules quickly formed within one month for both photobioreactors. IC-PMBR exhibited more excellent pollutants removal performance than IC-PSBR. The removal efficiencies of TN, PO43- and TOC in IC-PMBR were 95 ± 3%, 78 ± 6% and 85 ± 3%, respectively. The excellent nitrogen removal in both bioreactors was ascribed to the enrichment of Proteobacteria and Cyanobacteria. Interestingly, the increasing abundance of Leucothrix could enhance the denitrification in the IC-PMBR. The removal of phosphate was achieved by phosphate accumulating organisms (PAOs) (mainly Thiothrix) and cyanobacteria in the IC-PMBR, while only p-accumulation microalgae dominated the phosphate intake in the IC-PSBR. Moreover, the synergy of heterotrophic bacterial and microalgae improved the removal efficiency of organics in both bioreactors. Morphology observation and community analysis revealed that the key players in photogranules from IC-PMBR was Phormidium sp. acting as backbones and interweaving a mat on the surface of granules. In contrast, an integrated Leptolyngbya sp. with false branching was observed in photogranules from the IC-PSBR acting as an interior core and mat-like structure was absent. Noticeably, an anaerobic region was detected in photogranules from both bioreactors with different proportion, primary Rhodobacteraceae and Thiotrichaceae. Therefore, this study demonstrated that cultivating photogranules in continuous-flow membrane photobioreactor provided an alternative option for high saline wastewater treatment.