This paper presents a novel formation control method for a large number of robots or vehicles described by Euler-Lagrange (EL) systems moving in elliptical orbits. A new coordinate transformation method for phase synchronization of networked EL systems in elliptical trajectories is introduced to define desired formation patterns. The proposed phase synchronization controller synchronizes the motions of agents, thereby yielding a smaller synchronization error than an uncoupled control law in the presence of bounded disturbances. A complex time-varying and switching network topology, constructed by the adaptive graph Laplacian matrix, relaxes the standard requirement of consensus stability, even permitting stabilization on an arbitrary unbalanced graph. The proofs of stability are constructed by robust contraction analysis, a relatively new nonlinear stability tool. An example of reconfiguring swarms of spacecraft in Low Earth Orbit shows the effectiveness of the proposed phase synchronization controller for a large number of complex EL systems moving in elliptical orbits.