With the development of the space exploration technology and the increase of computer power, a series of numerical models for the middle atmosphere have been developed in recent years. In this paper, an informal brief survey of the current issues and challenges in the development of comprehensive middle and upper atmospheric models are presented and the current and future research applications of models for the middle atmosphere are discussed. At present, the middle atmosphere models developed from the state of art general circulation models typically have a domain extending from the ground up to stratosphere and the lower part of the mesosphere. Few such models have their model tops extending up to the thermosphere. The most existing models for the middle atmosphere have the ability of simulating reasonably the atmospheric chemical and dynamical processes in the stratosphere such as the time evolution of the Antarctic ozone hole and signals of Quasi-biennial Oscillation and semi-annual Oscillation in the equatorial stratosphere. However, uncertainties and differences in simulated results between models are still large. For the improvement of the middle atmosphere models, the radiation scheme and the gravity wave parameterisation scheme are the main focuses for physical processes, while the full coupling between atmospheric chemical and dynamical as well as micro-physical processes is another aspect of model development under way. Meanwhile, the description of chemical and physical processes above the stratosphere also needs improvement. The models for the middle atmosphere have wide applications in various atmospheric research fields. To further develop and improve such model is not only important for the weather and climate predictions but also useful for the research of the space science.