Pointing to marine greenhouse gas emissions, the EEDI (Energy Efficiency Design Index), a mandatory regulation, has become a significant factor in the design of ships’ hull lines. EEDI is closely related to many design parameters of ships’ hulls, which were conventionally set to be constant when involved in the design. However, it is often the case that considerable parameter fluctuations happen during actual navigation (such as travelling speed, draft, etc.), so it is more reasonable to state the important parameters as random variables. The reliability and quality level requirements of design results are also of concern. Accordingly, a reliability-based optimisation design (RBOD) method is introduced in this research. Furthermore, the design of experiments and reliability analyses via a Monte Carlo simulation and four reliability methods are employed to measure the sensitivity of the design variables and their reliability. Upon comparison with deterministic optimisation design (DOD) via adaptive simulated annealing (ASA), ROBD shows excellent adaptability and reliability in minimum EEDI ship hull lines’ designs.