Energy efficiency (EE) and spectrum efficiency (SE) have received significant attentions on optimizing the network performance in cognitive radio networks. In this paper, an EE+SE tradeoff based target is considered for the primary users (PUs) and the secondary users (SUs). First of all, considering the orthogonal frequency division multiple access-based resource allocation (RA) for the underlying SUs, we formulate an objective function through minimizing a weighted sum of the secondary interference power, where the network performance of both PUs and SUs are guaranteed by the constraints on quality of service, power consumption and data rate. However, it is a NP-hard problem. In order to solve it, we propose a damped three dimensional (D3D) message-passing algorithm (MPA) based on deep learning. Specifically, a feed-forward neural network is devised and an analogous back propagation algorithm is developed to learn the optimal parameters of the D3D-MPA. To improve the computational efficiency of the allocation and the learning, a suboptimal RA scheme is deduced based on a damped two dimensional MPA. Finally, simulation results are provided to confirm the effectiveness of our proposed scheme.