In space application, robot systems are subject to unknown or unmodeled dynamics, for example, in the tasks of transporting an unknown payload or catching an unmodeled moving object. We discuss the parameterization problem in dynamic structure and adaptive control of a space robot system with an attitude-controlled base to which the robot is attached. We first derive the system kinematic and dynamic equations based on Lagrangian dynamics and the linear momentum conservation law. Based on the dynamic model developed, we discuss the problem of linear parameterization in terms of dynamic parameters, and find that, in joint space, the dynamics can be linearized by a set of combined dynamic parameters; however, in inertial space linear parameterization is impossible in general. Then we propose an adaptive control scheme in joint space, and present a simulation study to demonstrate its effectiveness and computational procedure. Because most takes are specified in inertial space instead of joint space, we discuss the issues associated to adaptive control in inertial space and identify two potential problems: unavailability of joint trajectory because the mapping from inertial space trajectory is dynamic-dependent and subject to uncertainty; and nonlinear parameterization in inertial space. We approach the problem by making use of the proposed joint space adaptive controller and updating the joint trajectory by the estimated dynamic parameters and given trajectory in inertial space.