Ensuring the swift and precise tracking of power system signal parameters, especially the frequency, is imperative for the secure and stable operation of power grids. In instances of faults within the distribution network, abrupt changes in frequency may occur, presenting a challenge for existing algorithms that struggle to effectively track such signal variations. Addressing the need for enhanced performance in the face of frequency mutations, this paper introduces an innovative approach—the Covariance Reconstruction Extended Kalman Filter (CREKF) algorithm. Initially, the dynamic signal model of electric power is meticulously analyzed, establishing a dynamic signal relationship based on high-precision time source sampling tailored to the signal model’s characteristics. Subsequently, the filter gain, covariance matrix, and variance iteration equation are determined based on the signal relationship among three sampling points. In a final step, recognizing the impact of the covariance matrix on algorithmic tracking ability, the paper proposes a covariance matrix reset mechanism utilizing hysteresis induced by output errors. Through extensive verification with simulated signals, the results conclusively demonstrate that the CREKF algorithm exhibits superior measurement accuracy and accelerated tracking speed when confronted with mutating signals.