This paper employs a hybrid optimization algorithm with a combination of linear programming (LP) and nonlinear programming (NLP) to design the highly homogeneous superconducting magnets for magnetic resonance imaging (MRI). The whole work is divided into two stages. The first LP stage provides a global optimal current map with several non-zero current clusters, and the mathematical model for the LP was updated by taking into account the maximum axial and radial magnetic field strength limitations. In the second NLP stage, the non-zero current clusters were discretized into practical solenoids. The superconducting conductor consumption was set as the objective function both in the LP and NLP stages to minimize the construction cost. In addition, the peak–peak homogeneity over the volume of imaging (VOI), the scope of 5 Gauss fringe field, and maximum magnetic field strength within superconducting coils were set as constraints. The detailed design process for a dedicated 3.0 T animal MRI scanner was presented. The homogeneous magnet produces a magnetic field quality of 6.0 ppm peak–peak homogeneity over a 16 cm by 18 cm elliptical VOI, and the 5 Gauss fringe field was limited within a 1.5 m by 2.0 m elliptical region.