In recent years, the communication-protocol-based synthesis and analysis issues have gained substantial research interest owing mainly to their significance in networked systems. In this work, we survey the control and filtering problems of networked systems under the effects induced by communication protocols. First, we introduce the engineering background of networked systems as well as the theoretical frameworks established to deal with the communication-protocol-based analysis and synthesis problems. Then, recent advances (especially the latest results) are reviewed on the stability analysis issue subject to protocol scheduling. Subsequently, the particular effort is devoted to presenting the latest progress on various communication-protocol-based control and filtering problems according to the characteristics of networked systems (e.g. time-varying nature, random behaviours, types of parameter uncertainties, and kinds of distributed structure). After that, we provide a systematic review of the communication-protocol-based fault diagnosis problems. Finally, some research challenges of communication-protocol-based control and filtering problems are outlined for future research.