The efficient treatment of biogas slurry (BS) to meet the government’s discharge standards is a major challenge for most livestock and poultry enterprises. Although microalgae-based wastewater treatment has many significant benefits over traditional technologies, the poor ammonium tolerance of regular algal species, the pH imbalance during microalgae cultivation, and the complex and expensive BS pretreatment process greatly limit its application in BS treatment. Aimed at these issues, this study firstly isolated a robust Chlorella sp. with strong ammonium and acidic tolerance, as well as heterotrophy ability. To facilitate optimal pH stability and growth enhancement, a co-metabolism cultivation strategy based on the addition of 0.1 g·L-1 acetate in the form of fed-batch was developed. In addition, an efficient pretreatment process integrating ammonia reduction by air stripping with turbidity and chromaticity reduction by acidic precipitation was developed for the elimination of inhibitory factors of microalgal growth in BS. The isolated Chlorella sp. was capable of growing in the pretreated real BS and no growth inhibition was observed even in the undiluted BS. The acetate co-metabolism cultivation strategy obviously enhanced cell growth and pollutant removal and both NH4+ and total phosphorus were reduced to meet the discharge standards of China via 2.5-fold dilutions of BS. The accumulation of high-value biomass could not only fully cover the cost of wastewater treatment, but also bring significant returns. The net profit from treating 1 m3 of BS reached $ 116.2. This study provides a simple and efficient packaged process for the treatment of high strength BS and is expected to greatly reduce the process cost of BS.