With the increase of access point (AP) density and the exponential growth of mobile devices supported by ultra dense networks (UDNs), overlapped user-centric (UC) clustering is becoming a promising design principle for guaranteeing the quality of service (QoS) required by each UE. However, the overlapped UC clustering has to be jointly designed with resource allocation in UDNs. In this context, both the traffic-load balancing and the limited availability of orthogonal resource blocks (RBs) are carefully considered in UDNs. To tackle these challenges, we formulate a joint overlapped UC clustering and resource allocation problem with the goal of maximizing the system’s spectral efficiency (SE). With the aid of the graph-theoretical framework, the problem is decoupled into two independent subproblems, and a distributed overlapped UC clustering solution as well as a graph-based resource allocation scheme were proposed. Our numerical results quantify the superior performance of the proposed framework in terms of both its per area aggregated user rate (PAAR) and user rate.