[Background] Environmental factors and nutrient factors have significant effects on the growth and biochemical composition of microalgae, and light intensity and nitrogen concentration are two of important environmental factors. [Objective] The effects of different light intensities and initial nitrogen concentrations on the growth and biochemical composition of filamentous green alga, Zygnema sp. was investigated. [Methods] The alga was grown in bubble column glass photobioreactor with modified BBM medium under two light intensities (100 μmol/(m2·s) and 300 μmol/(m2·s)) and six initial nitrogen concentration gradients (3, 6, 9, 12, 15 and 18 mmol/L). [Results] The highest biomass was observed at high light intensity (300 μmol/(m2·s)) and 12 mmol/L initial nitrogen concentration, which was 6.60 g/L. The initial low nitrogen concentration (3 mmol/L) was conducive to the accumulation of total lipid and fatty acids of Zygnema sp., and the highest total lipid content reached 32.13% of dry weight. The main components of fatty acid were palmic acid, oleic acid, linoleic acid and α-linolenic acid, and oleic acid content accounted for 55.01% of total fatty acid. Under low light intensity (100 μmol/(m2·s)), the highest protein and carbohydrate content was obtained under 18 mmol/L initial nitrogen concentration, which was 16.35% of dry weight and 37.70% of dry weight, respectively. Meanwhile, the total lipid content accounted for only 10.16% of dry weight. [Conclusion] The light intensity and initial nitrogen concentration had a great influence on the growth and biochemical composition of Zygnema sp., the target accumulation of metabolites of Zygnema sp. could be effectively increased by adjust the light intensity and initial nitrogen concentration.