Interharmonic interference can significantly degrade the accuracy of synchrophasor estimation algorithms. With the widespread integration of power electronic devices, interharmonic interference has become one of the key bottlenecks restricting further improvements in synchrophasor estimation accuracy. To address this issue, this paper proposes a dynamic synchrophasor estimation algorithm based on matrix pencil frequency tracking. The algorithm performs frequency tracking based on the matrix pencil method and introduces threshold-based singular value screening to suppress noise and extract frequency components. Then, dynamic estimation of phasor parameters is carried out based on the Taylor series model and the symmetric characteristics of phasors. Finally, the estimation accuracy is further improved by iteratively reducing the interference of negative-sequence frequency components. Simulation results show that the proposed algorithm can achieve fast tracking of fundamental frequency and high-precision estimation of synchrophasor parameters, and can effectively suppress interharmonic interference in test scenarios containing interharmonics. The algorithm fully meets the performance requirements of M-class PMU specified in the IEEE/IEC 60255-118-1 standard, and meets the P-class PMU standard in most scenarios.