The Mine Internet of Things (MIoT), as an application paradigm of the IoT in mine environment, realizes the state perception and information interaction by connecting massive smart sensing devices deployed in mine, plays an important role in coal mine production. The fifth-generation (5G) is a key enabling technology to provide an efficient and reliable communication link guarantee for MIoT networks. To meet the increasing demand for huge amounts of data transmission, a NOMA-based heterogeneous MIoT communication system is proposed. In this paper, different types of mine smart devices can occupy the same subchannel resources for data transmission by the NOMA technology, which improves the device access and spectrum utilization of the MIoT system. We aim to maximize the energy efficiency (EE) of all small cell networks via power allocation and subchannel assignment. Under the imperfect channel state information (CSI), a joint power allocation and subchannel assignment iterative algorithm is proposed. Specifically, firstly, by considering the cross-layer interference power constraints, maximum power constraints and QoS constraints, the EE optimization problem is formulated as a mixed integer nonlinear fractional programming problem. Secondly, the uncertain CSI is modeled as an elliptical uncertainty set, and the original problem is transformed into an equivalent convex optimization form by using the Dinkelbach method. Finally, an approximate solution is obtained by using the Lagrangian dual approach. The numerical results validate the effectiveness of the proposed algorithm and significantly show its superior performance as compared with the baseline algorithms.