In order to effectively alleviate the problem of "abandoning wind and light" of new energy, a market bidding method for hydrogen chain of rivers and waterways based on a two-layer decision-making model is proposed. Firstly, the operation mechanism of the hydrogen chain of rivers and waterways is explained, and the decision-making structure for its participation in the hydrogen energy market is designed. On this basis, a bidding mechanism for hydrogen chain market in rivers and waterways based on a two-layer decision-making model is proposed. Among them, the upper level aims to maximize the daily operating income, and establishes a hydrogen chain operation model considering the fine power adjustment of hydrogen compressors. With the goal of maximizing social well-being, the lower level establishes a hydrogen energy market clearance model considering multi-agent bidding. Then, the model is reconstructed based on the KKT condition, and the model is transformed into a classic mix-integer linearization programming (MILP) problem by using duality theory and large M method to achieve efficient solution of the model. The results of case analysis show that compared with the traditional method, the proposed strategy can improve the operation economy of the system by no less than 5.4%. The proposed strategy provides a new perspective for hydrogen chain operation and hydrogen energy market trading.