Thirdly, we modify the Lotka-Volterra model to solve the main problems for polyculture. Simulation results show that the water quality can be improved high enough to reestablish the original reef ecosystem by itself. At the same time, we obtain economic value and water quality accordingly by changing the initial conditions. Furthermore, we discuss the harvesting of each species for human consumption, and construct an optimization model to maximize total value harvest with or without considering the water quality. To solve the constrained optimization, an algorithm OPTM is designed.