We explore the impact of pumping beams with different transverse intensity profiles on the performance of the spin-exchange relaxation-free (SERF) atomic magnetometers (AMs). We conduct experiments comparing the traditional Gaussian optically-pumped AM with that utilizing the flat-top optically-pumped (FTOP) method. Our findings reveal that the FTOP-based approach outperforms the conventional method, exhibiting a larger response, a narrower magnetic resonance linewidth, and a superior low-frequency noise performance. Specifically, the use of FTOP method leads to a 16% enhancement in average sensitivity within 1 Hz–30 Hz frequency range. Our research emphasizes the significance of achieving transverse polarization uniformity in AMs, providing insights for future optimization efforts and sensitivity improvements in miniaturized magnetometers.