Maritime pilotage is an important guarantee for the safety of water traffic in port. The pilot is affected by the complex port environment, the differences of crew and equipment of different ships, the physical and psychological pressure of the pilot himself, as well as the management factors from the pilot station and maritime safety administration. In order to avoid pilotage accidents (PAs), it is necessary to study the coupling effect of human-organizational factors (HOFs) on PAs. In this paper, from the perspective of HOF risk coupling in pilotage, the problem of HOF risk coupling in maritime pilotage is studied by using the hierarchical classification idea of the human factors analysis and classification system (HFACS) and the method of system dynamics (SD). First of all, HFACS is used to analyse the HOF risk causal elements (RCEs) in pilotage, and 70 RCEs are summed up in four layers; secondly, the SD coupling model of RCEs is constructed; finally, based on a dataset of PAs collected by the Shanghai Harbour Pilot Association, the coupling simulation of RCEs in pilotage is carried out, and the volatility is evaluated. In general, the safety situation of maritime pilotage has been improving in the Shanghai port. However, four RCEs (negligence, habit, pilotage experience, and violations) in unsafe acts and two RCEs (teamwork and personal safety awareness) in precondition for unsafe acts contribute the most to maritime PAs and need to be paid attention to.