Device-to-Device communications have the great potential to bring significant performance boost to the conventional heterogeneous network by reusing cellular resources. In cellular networks, Device-to-Device communication is defined as two user equipments in a close range communicating directly with each other without going through the base station, thus offloading cellular traffic from cellular networks. In addition to improve network spectral efficiency, D2D communication can also improve energy efficiency and user experience. However, the co-existence of D2D communication on the same spectrum with cellular users can cause severe interference to the primary cellular users. Thus the performance of cellular users must be assured when supporting underlay D2D users. In this work, we have investigated cross-layer optimization, resource allocation and interference management schemes to improve user experience, system spectral efficiency and energy efficiency for D2D communication underlaying heterogeneous networks. By exploiting frequency reuse and multi-user diversity, this research work aims to design wireless system level algorithms to utilize the spectrum and energy resources efficiently in the next generation wireless heterogeneous network.