The pollution and transformation of refineries are receiving increasing attention. The carbonic anhydrase in Tetradesmus obliquus was found exhibiting a hysteresis phenomenon in response to periodic changes in the composition of external carbon sources, with a surge in inorganic carbon concentration stressing the carbonic anhydrase activity to increase by 6–9 times. On this basis, a novel three-stage culture system of T. obliquus was proposed, which mainly uses refinery waste as the nutrients. By controlling the nutrient content in the environment, especially the composition of carbon sources, microalgae could sequentially complete rapid biomass accumulation, efficient inorganic carbon assimilation, and oil production. Compared to a single-environment culture system, the biomass yield increased by 1.34 times, the oil content increased by more than 6%, and the oil productivity increased by 2.08 times. Above findings may lay a partial theoretical foundation for the future evolution of traditional refineries towards “fossil–algal-biomass” hybrid refineries.