Waterway transportation plays an essential role for economic development. Maritime Safety Administration (MSA) shoulders the responsibility to maintain waterway transportation safety and efficiency and to avoid environmental contamination. This paper focuses on the assessment of MSA performance in term of safety with Belief Rule-base (BRB) methodology. A generalization of traditional BRB theories, which is called G-BRB, is introduced in this paper at first. G-BRB focuses on the fact that experts’ subjective standards on one quantitative attribute may be different. The qualitative data of safety and cost attributes from expert questionnaires is transformed into antecedent belief structure (A-BS), which can well reflect the distinctions among experts’ knowledge. The match degree and activation weight are then proposed to deal with A-BSs to make inference. After that, the proposed method is used to assess the performance of one MSA in China during the year 2007–2011. The factors used for MSA performance assessment are divided into two sub-groups and assessed separately. One group mainly focuses on safety situation and the other group pays attention to cost of maintaining safety. Then the outputs of the two sub-groups are used as the inputs for MSA performance assessment to get final results. After the comparison with experts knowledge (which is believed to be expert opinions of MSA performance), the results show that G-BRB can deal with experts’ different criteria on some factors successfully. The results also show that the proposed method performs well in terms of precision and reliability.