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BACKGROUND: Microalgal biodiesel is one of the best promising candidates as an alternative liquid fuel in response to the energy crisis. The timely development of cost‐effective and environmentally friendly culture systems for enhancing microalgae production on a commercial scale is extremely important. In this study, the effects of the process variables temperature, LED light source (blue, white, red), light intensity and aeration rate on biomass production, and the effects of the renewal rate and cycle time on the culture harvest of the marine microalga Isochrysis sp. were investigated using Box–Behnken design (BBD) and central composite design (CCD), respectively. RESULTS: The biomass productivity and lipid content of Isochrysis sp. significantly depended on temperature. Maximum biomass productivity was achieved under white LED light. The optimal conditions for biomass production of Isochrysis sp. with economic cost and energy consumption were a culture temperature of 35 °C, white LED illumination, light intensity 182 μmol m−2 s−1 and an aeration rate of 1.0 L L−1 min−1. A medium renewal rate of 30% and a culture harvest cycle time of three days resulted in the highest biomass productivity for Isochrysis sp. The respective biomass productivities predicted by the models were in good agreement with the results obtained in photobioreactor experiments. CONCLUSION: Major factors remarkably influenced the culture conditions and biomass harvesting. The results can offer a promising roadmap for the cost‐effective production of biodiesel using Isochrysis sp. © 2021 Society of Chemical Industry [ABSTRACT FROM AUTHOR]