The maneuvering target echo of high-resolution radar can be expressed as a multicomponent polynomial phase signal (mc-PPS). However, with improvements in radar resolution and increases in the synthetic period, classical time frequency analysis methods cannot satisfy the requirements of maneuvering target radar echo processing. In this paper, a novel frequency domain extraction-based adaptive joint time frequency (FDE-AJTF) decomposition method was proposed with three improvements. First, the maximum frequency spectrum of the phase compensation signal was taken as the fitness function, while the fitness comparison, component extraction, and residual updating were operated in the frequency domain; second, the time window was adopted on the basis function to fit the uncertain signal component time; and third, constant false alarm ratio (CFAR) detection was applied in the component extraction to reduce the ineffective components. Through these means, the stability and speed of phase parameters estimation increased with one domination ignored in the phase parameter estimation, and the accuracy and effectiveness of the signal component extraction performed better with less influence from the estimation errors, clutters, and noises. Finally, these advantages of the FDE-AJTF decomposition method were verified through a comparison with the classical method in simulation and experimental tests.