Due to the fast increase of sensing data and quick response requirement in the Internet of Things (IoT) delivery network, the high speed transmission has emerged as an important issue. Assigning suitable channels in the wireless IoT delivery network is a basic guarantee of high speed transmission. However, the high dynamics of traffic load (TL) make the conventional fixed channel assignment algorithm ineffective. Recently, the software defined networking-based IoT (SDN-IoT) is proposed to improve the transmission quality. Besides this, the intelligent technique of deep learning is widely researched in high computational SDN. Hence, we first propose a novel deep learning-based TL prediction algorithm to forecast future TL and congestion in network. Then, a deep learning-based partially channel assignment algorithm is proposed to intelligently allocate channels to each link in the SDN-IoT network. Finally, we consider a deep learning-based prediction and partially overlapping channel assignment to propose a novel intelligent channel assignment algorithm, which can intelligently avoid potential congestion and quickly assign suitable channels in SDN-IoT. The simulation result demonstrates that our proposal significantly outperforms conventional channel assignment algorithms.