This work focuses on topics related to Hamiltonian stochastic differential equations with Lévy noise. We first show that the phase flow of the stochastic system preserves symplectic structure, and propose a stochastic version of Hamilton's principle by the corresponding formulation of the stochastic action integral and the Euler-Lagrange equation. Based on these properties, we further investigate the effective behaviour of a small transversal perturbation to a completely integrable stochastic Hamiltonian system with Lévy noise. We establish an averaging principle in the sense that the action component of solution converges to the solution of a stochastic differential equation when the scale parameter goes to zero. Furthermore, we obtain the estimation for the rate of this convergence. Finally, we present an example to illustrate these results.