Recognition and correction of ionospheric phase path contamination is a vital part of the global radar signal processing sequence. A number of model-based correction algorithms have been developed to deal with the radar performance degradation due to the ionospheric distortion and contamination. This paper addresses a novel parametric estimation and compensation method based on High-order Ambiguity Function (HAF) to solve the problem of phase path contamination of HF skywave radar signals. When signal-to-noise ratio and data sequence available satisfy the predefined conditions, the ionospheric phase path contamination may be modeled by a polynomial phase signal (PPS). As a new parametric tool for analyzing the PPS, HAF is introduced to estimate parameters of the polynomial-phase model and reconstruct the correction signal. Using the reconstructed correction signal, compensation can be performed before coherent integration so that the original echo spectrum can be restored. A piecewise scheme is proposed to track rapid variation of the phase contamination based on HAF method, and it can remove the Doppler spread effect caused by the ionos phere nonstationarity. Simulation and experimental results are given to demonstrate the efficiency of the proposed algorithm.