Due to the complex intra-pulse modulation of polyphase code signals, most research on intra-pulse parameter estimation algorithms has focused on utilizing techniques such as the Wigner Hough transform (WHT), Radon Wigner transform (RAT), and other methods. In this paper, we studied the fractional Fourier transform (FRFT) normalized spectrum of polyphase coded signals and derived a mathematical model to prove the impulse characteristic of the polyphase coded spectrum under optimum order. This is the theoretical basis for the fourth-order origin moment as the objective function, and an algorithm based on FRFT is proposed to estimate the intra-pulse parameters of polyphase coded signals. Through simulation experiments, it was shown that the algorithm has a good parameter estimation effect and low computational time, making it suitable for engineering practice. Furthermore, considering the difficulty in obtaining prior information on parameters in non-cooperative environments, which leads to the inapplicability of evaluation standard such as mean square error (MSE), we proposed an evaluation standard for parameter estimation based on a posteriori models. Through simulation experiments, this standard was proven to be as persuasive as MSE.