A potential mixotrophy coupling transient N-deficiency two-step strategy (MCTN) was developed for concurrent accumulation of lipid and lutein in Chlorella protothecoides. The results demonstrated that C. protothecoides subjected to MCTN manipulation synchronously achieved favorable lutein productivity of 7.10 mg/L/d and lipid productivity of 557.66 mg/L/d. Whilst such strategy positively modulated the proportions of fatty acids with saturated C16:0 and C18:0 (19.67 %), monounsaturated C18:1 (47.13 %) and C18:3 (˂12 %), which were desirable for complying with the biodiesel quality specifications. Further, transcriptomics hinted that C. protothecoides treated with MCNT strategy employed special way that boosting supply of acetyl-CoA combining the regulations of key checkpoints (e.g. lycopene β,ε-cyclase, stearoyl-ACP desaturase, diacylglycerol acyltransferase) involved in respective pathway to coordinate co-accumulation of lipid and lutein. These encouraging findings not only provided indications for better understanding the trade-offs between lipid and lutein but also impelled this conducive strategy towards offsetting alga-based biodiesel production cost.