In this paper, a model of Beddington–DeAngelies chemostat involving two species of micro-organism competing for two perfectly complementary growth-limiting nutrients and pulsed input of toxicant in the polluted environment was studied. Using Floquet theory and small amplitude perturbation method, a conclusion was that there exists two-micro-organism eradication periodic solution and which is global asymptotical stability. At the same time, the condition of the permanence for system was obtained. From the biological point of view, the method for protecting species is to improve the amount of impulsive period, and control the amount of toxicant input to the chemostat. Finally, our results are illustrated by numerical simulations.