Ultra-Dense Network(UDN)，which is the key technology of 5G mobile communications, can greatly improve the network capacity and user throughput. However, the performance of UDN is limited seriously by inter-cell interference. To solve this problem in ultra-dense heterogeneous cellular network， a joint radio resource allocation algorithm is presented. In order to maximize system's energy efficiency while satisfying the Quality of Service(QoS) requirement of users，joint radio resource(i.e.，time-frequency and power resources) allocation is modeled as a combinatorial optimization problem with multiple constraints. However, this is a Non-deterministic Polynomial hard(NP-hard) problem which is difficult to be solved. A novel optimal algorithm is presented. Firstly，time and frequency resources are allocated based on enhanced Simulated Annealing algorithm(SA)，where particles deleting and tempering are introduced to improve the convergence speed and to avoid the local optimum. Secondly，power resources are alloated based on Lagrange multiplier method. Finally，global optimum is approached through multiple iterations. Simulation results show that the proposed scheme can ensure the fairness of users and improve the energy efficiency and network throughput effectively with faster convergence speed and higher convergence accuracy.