In this paper, multiple device-to-device (D2D) communication underlaying cellular multiuser multiple inputs multiple outputs (MU-MIMO) systems is investigated. This type of communication can improve spectral efficiency to address future demand, but interference management, user clustering, and resource allocation are three key problems related to resource sharing. Interference alignment (IA) is proposed to better mitigate in-cluster interference compared with a multiplex scheme, and user clustering and resource allocation are jointly investigated using binary-integer programming. In addition to an exhaustive search for a maximum throughput, we propose a two-step suboptimal algorithm by reducing the search space and applying branch-and-bound searching (BBS). To further obtain a good trade-off between performance and complexity, we propose a novel algorithm based on distance-constrained criteria for user clustering. The simulation results show that the IA and multiplex schemes acquiring user clustering gains outperform the orthogonal scheme without user clustering. Besides, the proposed two-step and location-based algorithms achieve little losses compared with the optimal algorithm under low complexities.