Effects of nitrogen-limitation and phosphorus-limitation on microcystin (MC) content and energy charge (EC) of the Microcystis aeruginosa were investigated in batch cultures and semi-continuous cultures. In batch cultures, nitrogen-limitation retarded the MC synthesis and phosphorus-limitation had little effects on MC production. The EC remained constant in nitrogen-limited cultures, while it decreased largely when phosphorus was extinct in phosphorus-limited culture. In the semi-continuous cultures, MC production in nitrogen- and phosphorus-limited cultures increased with the increase of dilution rate; however, MC content in phosphorus-limited cultures was more than that in nitrogen-limited cultures. The EC in nitrogen-limited cultures remained constant and in phosphorus-limited cultures increased with the increase of dilution rate. In phosphorus-limited semi-continuous cultures, a direct relationship between EC and MC content was demonstrated. No correlation was observed in nitrogen-limited semi-continuous cultures. Based on the above analysis, a mechanism of nitrogen and phosphorus effect on the MC synthesis was suggested, that the MC synthesis was determined by the combination of necessary enzymes and precursors and EC.