The levels of informatization, automation, and intelligence are continuously improving; however, the risks due to the increased design and operational complexity of ship systems are increasing. Large-scale ship accidents occur for various reasons. Existing accident analysis methods that examine marine accidents from the perspective of causal one-to-one correspondence have limitations in systematically analyzing complex marine risks when identifying their causes for the prevention of similar accidents. This study focuses on a systematic causality analysis of the factors related to human errors in marine accidents that may occur during the arrival and departure of mega container ships. In particular, a representative case of the Milano Bridge crane contact accident at Busan New Port is considered. To explore the complex organizational–technical, human–technical, and organizational–human relationships relevant to this case, human factors (seafarer, pilot, etc) that are closely related to the linked causes were analyzed using the functional resonance analysis method. This study aims to reduce human error and prevent marine accidents including pilotage.