The extraction of rare earth elements (REEs) through in-situ leaching with ammonium sulphate [(NH4)2SO4] had resulted in the production of a large volume of ammonium-rich wastewater, causing severe environmental pollution. This study aimed to assess the ability of an indigenous microalga Chlamydomonas sp. YC, isolated from REEs wastewater, to directly treat real REEs wastewater under outdoor conditions in 50 L airlift photobioreactors (AL-PBRs) and 5.0 m3 open race-way photobioreactors (ORWPs). Additionally, the harvested Chlamydomonas sp. YC biomasses from these two pilot photobioreactors were comprehensively analyzed to evaluate the nutritional values. The results showed that Chlamydomonas sp. YC in AL-PBRs exhibited higher biomass production (1.1 g/L), greater removal efficiencies in NH4+-N (24.9%) and total nitrogen (20.4%), as well as higher CO2 fixation rate (125.0 mg/(L·d)), compared to those of ORWPs. Moreover, the Chlamydomonas sp. YC biomasses obtained from the two pilot photobioreactors contained 44.5% and 49.4% protein, 9.1% and 14.3% lipids. Moreover, Chlamydomonas sp. YC in the two pilot photobioreactors displayed essential amino acid indexes (EAAI) of 0.900, which was higher than that of soybean protein (0.657), indicating superior nutritional values. In conclusion, the implementation of the process involving Chlamydomonas sp. YC in AL-PBRs under outdoor conditions holds promise as a coupled microalgal biotechnology for the simultaneous removal of NH4+-N from REEs wastewater, and the capture of CO2 for the production of valuable biomass.