The Single Cell Research Center of CAS Qingdao Institute of Bioenergy and Processes and the CAS Dalian Institute of Chemical Physics have developed an industrial oil-producing microalgae cell factory with high MCT production. Nannochloropsis spp. is an industrial oil-producing microalgae which can be “custom designed” for the length of fatty acids. Only two type II diacylglycerol acyltransferases (NoDGAT2) in Microcystis aeruginosa are capable of assembling MCFA into MCT through MCFA-mediated yeast heterologous expression and in vitro enzymatic assays. Subcellular localization experiments further demonstrated that both DGAT2 are involved in TAG assembly on chloroplasts. Further, the transcriptional levels of these two DGAT2s were rationally regulated in Microcystis aeruginosa and combined with the expression of several other exogenous MCT synthases to construct an engineered strain with high MCT production. At the peak oil production stage, the MCT content of the engineered algal strain was 64.8-fold higher than that of the wild type.