We establish a canonical decomposition of the infinitesimal Koopman generator of any port-Hamiltonian (pH) system into skew-adjoint (energy-conserving), positive-semidefinite (dissipative), and input-port components, proving that the generator satisfies an energy-dissipation inequality on a dense subdomain of $L^2(\mu)$ for any invariant measure $\mu$ satisfying a mild joint-invariance condition stated in Theorem 1. This infinite-dimensional splitting carries over exactly to finite-dimensional Galerkin approximations, yielding structure-constrained surrogate models that provably inherit passivity with a quadratic storage function in the lifted observable space. Leveraging this structure, we design passivity-based controllers directly in the lifted space and establish asymptotic stability of the lifted closed-loop system via LaSalle's invariance principle under a mild detectability condition. For linear pH systems, the decomposition recovers the true pH matrices exactly, confirming that the structural constraints arise naturally from the operator theory rather than being imposed by hand. The framework unifies port-Hamiltonian systems theory and Koopman spectral methods, providing a rigorous operator-theoretic foundation for energy-consistent lifting of nonlinear pH dynamics.