Containerization is a lightweight application virtualization technology, providing high environmental consistency, operating system distribution portability, and resource isolation. Existing mainstream cloud service providers have prevalently adopted container technologies in their distributed system infrastructures for automated application management. To handle the automation of deployment, maintenance, autoscaling, and networking of containerized applications, container orchestration is proposed as an essential research problem. However, the highly dynamic and diverse feature of cloud workloads and environments considerably raises the complexity of orchestration mechanisms. Machine learning algorithms are accordingly employed by container orchestration systems for behavior modelling and prediction of multi-dimensional performance metrics. Such insights could further improve the quality of resource provisioning decisions in response to the changing workloads under complex environments. In this paper, we present a comprehensive literature review of existing machine learning-based container orchestration approaches. Detailed taxonomies are proposed to classify the current researches by their common features. Moreover, the evolution of machine learning-based container orchestration technologies from the year 2016 to 2021 has been designed based on objectives and metrics. A comparative analysis of the reviewed techniques is conducted according to the proposed taxonomies, with emphasis on their key characteristics. Finally, various open research challenges and potential future directions are highlighted.