► Cane molasses can be transformed by Chlorella to oils and astaxanthin. ► Molasses with metal removal supported better growth than glucose. ► Crude molasses could be directly used by optimizing culture conditions. ► Molasses up-regulated key enzymes involved in oil and astaxanthin biosynthesis. ► Typing oils to astaxanthin enables profitable biodiesel from algae. The aim of this study is to evaluate the industrial waste cane molasses as a carbon source for cell growth, lipid and astaxanthin production of Chlorella zofingiensis. Pretreated with cation exchange resin to remove the metal ions, cane molasses provided better productivities of biomass, lipid, and astaxanthin (1.55, 0.71gL−1day−1 and 1.7mgL−1day−1, respectively) than glucose. Using a strategy of semi-continuous cultures coupled with feeding at a low concentration, molasses without pretreatment has the same effect as pretreated one on supporting the algal cell growth, lipid and astaxanthin production. The efficient metabolism of molasses triggered the up-regulation of genes involved in fatty acid and also astaxanthin biosynthesis, leading to the very high production of the two metabolites. This study highlights the possibility of using C. zofingiensis to deal with industrial wastes and to produce profitable biodiesel as well as the high-value astaxanthin.