Abstract: This paper proposes a model of relay cooperative multi-tier heterogeneous networks (HetNets), which consists of different types of relays and user pairs communicate with each other through the relay. All network elements are modeled as independent Poisson point process (PPP). Different from the traditional single-hop network, the user-pair associated depending on dual-hop link. To this end, the paper proposes a maximum-minimum user-pair association (MM-UPA) criterion against this novel network. Meanwhile, in order to overcome the bottleneck effect of MM-UPA criterion, a new UPA scheme which called maximum harmonic mean user-pair association (MHM-UPA) is further proposed in this paper, and this MHM-UPA criterion considers jointly dual-hop link. Posteriorly, by means of stochastic geometry and PPP, the user pair association probabilities of MM-UPA and MHM-UPA scheme are obtained, respectively. In the end, as an implementation of the proposed UPA criterions, the physical layer security of the considered HetNets is investigated, and the total average security probabilities are gained. The results show that proposed two UPA criterions consider jointly the performance of the source-relay and relay-destination two-hop links, and both are superior to single-hop user association scheme, so are suitable for relay assisted multi-tier HetNets.