According to the concept of independent set, this paper proposes a new immunization strategy of complex networks which immunizes the nodes in an independent set with maximum degree, called targeted immunization in the independent set. When the total degree of immune nodes in independent set is equal to the total degree of targeted immunization nodes in the whole network, the immunization strategy of independent set is more effective than the targeted immunization strategy of the whole network. Based on the network structure, this paper explains the reason. Comparing the random immunization of independent sets with the random immunization in the whole network, test results indicate that more nodes do not be removed with high degree for the random immunization of independent sets. For classic susceptible-infected(SI) model, all nodes in the network are only two states: susceptible or infected. In the study of immunization strategies, comparing SI model with SIR, SIS models. The use of SI model will be more favorable.