Background Microalgae can synthesize and accumulate various components that can be used in health supplements, pharmaceuticals, cosmeceuticals, and other bioproducts. Arachidonic acid (AA) is an omega-6 long-chain polyunsaturated fatty acid and is important for human health. The coccoid green microalga Lobosphaera bisecta SAG2043 has been reported to be able to accumulate high AA content under certain conditions. We evaluated the interactive effects of nitrogen concentration, light intensity, and medium replacement on the growth and accumulation of lipids and AA in this strain. We further performed transcriptome analysis on L. bisecta in order to elucidate the mechanism of AA and triacylglycerol (TAG) metabolism under nitrogen deficiency. Results Nutrient management and light intensity had significant effects on the biomass and accumulation of lipids and AA in L. bisecta. Both a high nitrogen concentration (18 mM) and high light intensity (bilateral light-300 μmol m -2 s -1 ) were beneficial to the growth of L. bisecta, and the replacement of culture medium further enhanced the biomass, which eventually reached 8.9 g L -1 . Low nitrogen concentration (3.6 mM) and high light significantly promoted the accumulation of lipids and AA. The highest lipid and AA content reached 54.0% and 10.8% of dry weight, respectively. Lipid compositions analysis under low nitrogen concentration showed that neutral lipids comprised 86.5% of the total lipids, and 88.2% of AA was distributed within the neutral lipids. We then reconstructed the lipid metabolic pathways of L. bisecta for the first time, and demonstrated that upregulation of a key desaturase and elongase in the Δ6 pathway was conducive to the accumulation of fatty acids toward AA synthesis. The synthesis of oleic acid, especially, ensured an adequate supply of precursor for AA synthesis. In addition, crucial genes within the TAG synthesis pathway were also up-regulated. Conclusion L. bisecta SAG2043 exhibits rapid growth, and high lipid and AA production. It may be a potential candidate for AA production. Transcriptome analysis showed that multi-level regulation ensured the conversion efficiency from carbon to the synthesis of fatty acids, which significantly promoted the accumulation of AA and TAG in L. bisecta.