Passive shimming is widely used in magnetic resonance imaging (MRI) systems due to its excellent efficacy and cost-effectiveness. However, conventional shim tray structures have difficulty in effectively adjusting magnetic field distributions under specific conditions. This limitation can lead to insufficient cancellation of harmonics and result in significant residual forces on the trays, impeding accurate placement of the trays. In this study, instead of using the conventional design of the shim tray slot, we propose a dedicated passive shimming tray tailored for 3T cryogen-free animal MRI superconducting magnets. Passive shimming experiments were conducted to evaluate the performance of this novel design, in which we were able to improve the peak-to-peak magnetic field homogeneity within the 180 mm diameter imaging region, reducing peak-to-peak (p–p) variation from 349.35 ppm to 19.08 ppm. Furthermore, the p–p homogeneity of the magnetic field measured at the imaging area with a diameter of spherical volume (DSV) of 160 mm reached 8.67 ppm. In addition, we strictly controlled the residual magnetic force of the shim tray to ensure its accurate placement. The experimental results indicate that the proposed structural optimization method and the residual magnetic force control strategy show potential in high-field MRI instruments requiring high homogeneity and handling of high residual magnetic force.