Microcystis aeruginosa is a cyanobacterium species that can form harmful algal blooms in freshwater bodies worldwide. The use of caffeine to control nuisance algae by allelopathic inhibition will be environmentally friendly and promising. Caffeine removed successfully upto 82% of Microcystis aeruginosa at the following optimal conditions: pH 8, upto 25 °C of temperature, 100 rpm of mixing rate, 30 min of mixing time. These results was indicated that the amount of 2 g/L caffeine was removed 1g dryweight/L of Microcystis aeruginosa. The kinetic data showed substrate inhibition kinetics and maximum growth rate was obtained when the Microcystis aeruginosa was grown in medium containing 0.7 g/L of initial concentration of caffeine. Different substrate inhibition models were fitted to the kinetic data and found the Luong model was best. The model predicted kinetic parameters were in agreement with the experimental findings. The caffeine can be a promising inhibition due to its high efficiency and low dose requirements.