Inverse synchronization of hyperchaotic systems with heterogeneous structure is investigated. The parameters of feedback gain matrix are optimized by using quantum genetic algorithm (QGA), which overcomes the difficulty of parameter tuning in feedback gain. Numerical simulation results show that the QGA combining with the feedback inverse synchronization method can make the hyperchaotic Chen system and Lorenz system of the heterogeneous structure achieve inverse synchronization quickly in a short time, which shows the superiority of the algorithm, and verifies the feasibility and effectiveness of QGA in solving the inverse synchronization problem of heterogeneous structure.