This study investigated how the human central nervous system organizes complex three-dimensional (3D) ball-throwing movements that require both speed and accuracy. Skilled baseball players threw a baseball to a target at three different speeds. Kinematic analysis revealed that the fingertip speed at ball release was mainly produced by 1) trunk leftward rotation, 2) shoulder internal rotation, 3) elbow extension, and 4) wrist flexion in all speed conditions. The study participants adjusted the angular velocities of these four motions to throw the balls at three different speeds. We also analyzed the dynamics of the 3D multi-joint movements using a recently developed method called "non-orthogonal torque decomposition" that can clarify how angular acceleration about a joint coordinate axis (e.g., shoulder internal rotation) is generated by the muscle, gravity, and interaction torques. We found that the study participants utilized the interaction torque to generate larger angular velocities of the shoulder internal rotation, elbow extension, and wrist flexion. To increase the interaction torque acting at these joints, the ball throwers increased muscle torque at the shoulder and trunk but not at the elbow and wrist. These results indicate that skilled ball throwers adopted a hierarchical control in which the proximal muscle torques created a dynamic foundation for the entire limb motion and beneficial interaction torques for distal joint rotations.