External forces and environments can destabilize the floating crane's performance and inflict a high risk of failure in operation. Considering this, the effect of the suspended module during the lifting operation in sea waves is investigated to evaluate the dynamic response of the floating crane. In this article, the combination of potential flow theory in the Boundary Element Method (BEM) and an empirical model is proposed for the prediction of coupled motion on the floating crane and suspended module. Calculations of multibody systems are solved using the coupled motion formula based on the frequency domain method. An analysis of the lifting operation under beam waves is examined with two variations in the weight of the suspended module. The motion characteristics are depicted with the response amplitude operator (RAO) on the nine rigid body degrees of freedom. The resonances of peak frequency occurred in the floating crane's responses due to the lifting load system. The peak frequency of the roll response on the floating crane shifted to a higher frequency due to the impact of the pendulum motion. The difference in peak response of roll motion between variations of suspended load is about 25.8 %. The acceleration response of the suspended module in the z-direction for the large module presented a lower peak frequency than the smaller module.