This study presents a novel dual phase-locked loop two-dimensional synchronized motion modulation (TDSMM-DPLL) system designed to enhance the low-frequency detection capability of magnetoresistive (MR) sensors by effectively mitigating 1/f noise. The TDSMM-DPLL system integrates a comb-driven resonator and a piezoelectric cantilever beam resonator, achieving synchronized magnetic field modulation through a DPLL circuit that adjusts the resonant frequency of the comb-driven resonator to twice that of the cantilever beam resonator. Theoretical analysis and finite element simulations demonstrate a modulation efficiency of 38.98%, which is significantly higher than that of traditional one-dimensional modulation methods. Experimental validation confirms the system’s effectiveness, showing a 3.13-fold reduction in frequency Allan variance, decreasing from 217.32 ppb to 69.46 ppb, indicating substantial noise suppression. These results highlight the TDSMM-DPLL system’s potential to improve the performance of MR sensors in low-frequency applications, making it a promising solution for high-precision magnetic field detection.