A servicing spacecraft motion control approach for the problem of on-orbit truss structure assembly is developed in this paper. It is considered that a cargo container with a rod set and servicing spacecraft are in orbit initially. The assembly procedure is based on spacecraft free-flight motion between the structure’s specified points. The spacecraft is equipped with two robotic manipulators capable of attaching to the structure and holding rods. In addition, the spacecraft can repulse from the structure with a given relative velocity using a manipulator, so the spacecraft and the structure receive impulses. The repulsion velocity vector is calculated in order to reach the structure target point to deliver and install the rod into the truss structure, or to reach the cargo container and take a rod. The problem of searching the repulsion velocity is formulated as an optimization problem with constraints, taking into account the limited value of the repulsion velocity, collision avoidance with structure, restrictions on the angular velocity and translational motion of the structure in the orbital reference frame. This problem is solved numerically with an initial guess vector obtained analytically for simplified motion cases. The application of the proposed control scheme to the assembly of a truss-based antenna is demonstrated. It is shown that the servicing spacecraft is successfully transferred between the structure points by means of manipulator repulsion. Main features and limitations of the assembly problem using a spacecraft with two manipulators are discussed.