Brewery effluent (BE) as an appreciable and sustainable resource presented new possibilities in low-cost algal biomass production, whereas the relatively low essential macronutrients hindered extensive applications as growth medium for microalgae cultivation. The objective of this study was to investigate the feasibility of an integrated treatment strategy initiated by BE coupling phytohormones in augmenting biomass and lipid accumulation in Coccomyxa subellipsoidea. Results revealed that BE coupling synthetic 1-naphthaleneacetic acid (NAA) accomplished the favorable lipid productivity of 481.76 mg/L/days, representing 6.80- to 9.71-fold more than that of single BE as well as standard Basal media. BE coupling NAA feeding also heightened the proportions of C16-C18 fatty acids (over 96%) and mono-unsaturated C18:1 (approximate 45%) which were prone to high-quality biofuels-making. Such profound lipids accumulation might be attributable to that BE coupling NAA treatment drove most of metabolic flux (i.e. acetyl-CoA) derived from TCA cycle and glycolysis flowing into lipid accumulation pathway. Concurrently, the complete removal of total nitrogen and total phosphorus by C. subellipsoidea with assistance of NAA were easily complied with the permissible dischargeable limits for BE. These present results strongly demonstrated that BE coupling NAA was a potential feeding strategy in boosting algal lipid productivity and further provided great possibilities in linking affordable algal biomass production with high-efficient biological contaminants removal.