The invention discloses a preparation method and system of recombinant adeno-associated virus (rAAV), and recombinant bacmid. The method comprises: (1) separately preparing shuttle plasmids and a corresponding recombinant bacmid containing baculovirus genome; (2) integrating a rAAV core expression element which has a heterologous functional gene fragment with other expression cassettes which produce functional protein components necessary for rAAV so as to obtain a recombinant bacmid containing recombinant baculovirus genome producing the rAAV; and (3) transfecting the obtained recombinant bacmid into a host cell line for culturing. The system comprises the shuttle plasmids and the corresponding recombinant bacmid containing the baculovirus genome. The recombinant bacmid comprises at leastone expression cassette that produces functional protein components necessary for rAAV. The system has flexibility, compatibility, and higher passage stability.