Ultra-densification of radio access network (RAN) is essential to efficiently handle the ever-increasing mobile data traffic. In this paper, a joint multi-layered user clustering and scheduling is proposed as an inter-cluster interference coordination scheme for ultra-dense RAN using cluster-wise distributed MIMO transmission/reception. The proposed joint multi-layered user clustering and scheduling consists of user clustering using the K-means algorithm, user-cluster layering (called multi-layering) based on the interference-offset-distance (IOD), cluster-antenna association on each layer, and layer-wise round-robin-type scheduling. The user capacity, the sum capacity, and the fairness are evaluated by computer simulations to show the effectiveness of the proposed joint multi-layered user clustering and scheduling. Also shown are uplink and downlink capacity comparisons and optimal IOD setting considering the trade-off between inter-cluster interference mitigation and transmission opportunity.