Protocol is the lifeline of computer network. The rapid increasing of protocol complexity results in a discipline of protocol engineering. Based on an analysis of the contents and methods of protocol engineering activities and their interrelations, first discusses main formal description techniques (FDTs) and their characteristics, compares corresponding strongpoints and weaknesses, and then leads to Petri nets based FDT. Secondly, the paper points out special advantages of the Petri nets based formal techniques and the current research difficulties in Petri nets based protocol engineering, among which protocol development oriented net tools are now very important research tasks. Thirdly, the paper summarizes international research advances in terms of OSI/RM layers and expounds research trends in this area. Finally, the authors give fundamental methodologies for Petri nets based protocol engineering in protocol specification, verification and analysis, and computer-aided testing and implementation.