The dynamic response of moored crane-ship is studied. Governing equations for the dynamic response of a crane-ship coupled with the pendulum motion of the payload are derived based on Lagrange’s equations. The boom is modeled based on finite element method, while the payload is modeled as a planar pendulum of point mass. The dynamic response was studied using numerical method. The calculation results show that the large-amplitude responses occur at wave periods near the natural period of the payload. Load swing angle is smaller for crane-ship with flexible boom, in comparison with rigid boom. The ship surge mo- tions have large vibrations for crane-ship with flexible boom, which were not observed for a rigid boom. The analysis identifies the significance of key parameters and reveals how the system design can be adjusted to avoid critical conditions.