Shipboard carbon capture is a promising solution to help reduce carbon emissions in international shipping. In this work, we propose a data-driven dynamic modeling and economic predictive control approach within the Koopman framework. This integrated modeling and control approach is used to achieve safe and energy-efficient process operation of shipboard post-combustion carbon capture plants. Specifically, we propose a deep neural Koopman operator modeling approach, based on which a Koopman model with time-varying model parameters is established. This Koopman model predicts the overall economic operational cost and key system outputs, based on accessible partial state measurements. By leveraging this learned model, a constrained economic predictive control scheme is developed. Despite time-varying parameters involved in the formulated model, the formulated optimization problem associated with the economic predictive control design is convex, and it can be solved efficiently during online control implementations. Extensive tests are conducted on a high-fidelity simulation environment for shipboard post-combustion carbon capture processes. Four ship operational conditions are taken into account. The results show that the proposed method significantly improves the overall economic operational performance and carbon capture rate. Additionally, the proposed method guarantees safe operation by ensuring that hard constraints on the system outputs are satisfied.