The Rb polarization-induced magnetic field gradient affects the Xe nuclear spin relaxation properties and degrades the long-term stability of the NMR co-magnetometers. This paper proposes a combination suppressing scheme, which uses the second-order magnetic field gradient coils to compensate for the Rb polarization-induced magnetic gradient under counter-propagating pump beams. Based on the theoretical simulation, we find that the spatial distribution of the Rb polarization-induced magnetic gradient and the magnetic field distribution generated by gradient coils are complementary. The experimental results indicate that the compensation effect is 10% higher under the counter-propagating pump beams scheme compared with the compensation effect under the conventional single beam. Besides, due to a more uniform spatial distribution of electronic spin polarization, the Xe nuclear spin polarizability is improved and the signal-to-noise ratio (SNR) of NMR co-magnetometers could be further enhanced. The study provides an ingenious method for suppressing magnetic gradient in the optically polarized Rb-Xe ensemble, which is expected to improve the performance of the atomic spin co-magnetometers.