Electric furnace slag was highly productive and rich in elements, which can be used as a nutrient source for microalgae growth. The regulation of growth and lipid synthesis of Chlorella pyrenoidosa (C. pyrenoidosa) in electric arc furnace slag leaching solution with or without citric acid was investigated to develop efficient lipid production method with low cost. High lipid content of 45.89 wt% from C. pyrenoidosa with adding electric arc furnace slag leaching solution ≤40% into BG11 was obtained due to C. pyrenoidosa increasing lipid accumulation to resist oxidative stress caused by heavy metals in electric arc furnace slag (Ca of 5.13 mg/L, Fe of 0.05 mg/L, Mn of 0.12 mg/L and Cr of 0.01 mg/L). Exogenous citric acid can improve the ability of C. pyrenoidosa to resist heavy metal toxicity with high biomass content (0.44 g/L) achieved. The cooperation of multiple metal ions in electric arc furnace slag shortened the biomass accumulation stage and prolonged and speeded up the lipid synthesis stage of C. pyrenoidosa by modulating PEPC, ACC and ME activities. This study provided guidance for the industrialization of low-cost lipid-rich microalgae and metallurgical solid waste treatment.