This paper designs a synchronous controller to realize the function projective synchronization of the different structures, and applies the Lyapunov principle to the stability of the system. Simultaneously, the linearity independence of the coefficient vector of the uncertain parameters in the QCNN system is deduced, and the estimation of the uncertain parameters is realized. Both theoretical and simulated results demonstrate that the function projective synchronization of the two different structures hyperchaotic systems are scientific rationality. Also the uncertain parameters return to the ideal values gradually. The research results provide theoretical guidance for the application of nanoelectronic chaotic system in secure communication and image encryption.