The rigid-flexible coupled spacecraft, composed of flexible solar panels and a multilink manipulator, has gained prominence in on-orbit servicing due to rapid advancements in space technology. However, the intricate effects of rigid-flexible coupling pose significant challenges for dynamic modeling, trajectory planning, and control. This paper aims to develop general dynamic approaches for modeling and trajectory planning in such spacecraft, considering large deformations. The main distinguishing feature is the use of the referenced nodal coordinate formulation to accurately describe the large-deformed solar panels rather than directly treating them as disturbance for the free-floating system. Additionally, the common recursive model for the multilink manipulator is integrated into the same framework. The modal reduction method with modal derivatives techniques is employed to address geometric nonlinearity resulting from large deformations. Polynomial trajectory parameters with different performance characteristics are obtained by defining various optimization objectives. The coupling analysis is conducted based on an accurate reduced-order dynamic model, the results of which can be used for designing manipulator tasks. Coupling values are defined as the objective for trajectory optimization, offering advantages such as insensitivity to dynamic model accuracy and a fast optimization process. After validating the accuracy of the proposed dynamic model through simulations, the performances of different optimized trajectories are demonstrated using numerical examples.