A class of non-uniformly sampling system is investigated, and the lifted state space model of non-uniformly sampled-data system is derived by using integration method. The corresponding transfer function model is further obtained. To solve the problem that there exist unknown mid-variables in information vectors of identification model, the auxiliary model technique is applied to replace the unknown system variables. The auxiliary models based instrumental variable identification algorithm of non-uniformly sampled-data system is presented. At last, a numerical example is given to illustrate the proposed method is effective.