In the port domain, quayside container cranes are an indispensable component of maritime freight transport. These cranes are not only costly but also associated with safety accidents that often result in casualties and property loss, severely impacting port operations and the surrounding environment. Given their complex operational environment, rapid technological updates, high dependency on human factors, and the challenges of maintenance and inspection, the safety of quayside container cranes is a significant concern for port enterprises and managers. This paper, based on the operational modes and structural characteristics of the cranes, divides them into five main systems and identifies twenty-eight safety evaluation indicators, covering a comprehensive range of risk factors from equipment integrity to operator behavior, as well as environmental factors. However, numerous pain points exist in the safety risk evaluation process of quayside container cranes, such as fuzziness, uncertainty, and complex multi-criteria decision-making (MCDM) environments. These issues make traditional safety evaluation methods inadequate in accurately reflecting the actual safety conditions. Therefore, this paper proposes a safety evaluation method for quayside container cranes based on the Best–Worst Method (BWM) and Pythagorean hesitant fuzzy VIKOR. This method effectively overcomes the uncertainties and fuzziness of traditional safety evaluation methods by integrating the decision maker’s preference information from the BWM and the fuzzy handling capability of Pythagorean hesitant fuzzy sets, enhancing the accuracy and reliability of the evaluation results. A case study was conducted on a quayside container crane at a specific port. Through empirical analysis, the feasibility of the proposed method was validated. Overall, the safety evaluation method for quayside container cranes based on the BWM and Pythagorean hesitant fuzzy VIKOR proposed in this paper enriches the theoretical research on the safety risk assessment of quayside container cranes and offers a new approach and tool for port enterprises and managers in practice.