The Doppler spectra of first-order sea echo are studied in a high frequency radar system for hybrid sky-surface wave propagation when the receiving antenna array is mounted on a shipborne platform. Here, the platform motion and ionosphere perturbed phases are assumed to be the key factors resulting in the sea clutter spectral fluctuation. Based on the received first-order electric field equation, a closed form of cross sections is derived to account for the ship motion influence. It is shown numerically that the resultant clutter spectra exhibit significant discrepancies with different system operating parameters and platform motion states. In addition, the phase path variations along the inhomogeneous ionosphere are considered by dividing the ionosphere into the quiescent and distorted components. Such manipulation makes it feasible to simulate the phase fluctuations with a method associated with deterministic and stochastic models. Eventually, simulation results for a composite modulation taking account of both effects are provided. Compared with the spread Doppler spectra due to the platform motion, the attached ionosphere perturbed phases will further split and leak the spectral energy, which may bring in difficulties for the applications in remote sensing and target detection.