One barrier, preventing the wide applications of elastic metamaterials (EMMs), is their limited ability to attenuate waves at low frequencies. Rainbow metamaterials (RMs), characterized by spatially varying structural parameters, can exhibit outstanding performance, boosting wider wave attenuation frequency ranges (stopbands) at lower frequencies compared to their counterparts of finite EMMs. However, attributed to the intricate topologies and constitutive relationships in 3D RMs, effectively configuring them to achieve enhanced wave-suspending capability is challenging. In most existing design approaches, frequency response analysis (FRA) method is frequently employed to iteratively calculate reliable stopband characteristics, leading to a significant computational burden. Herein, to address these challenges, a novel mode conversion approach is developed, underpinned by a recently proposed modal-based evaluation method (MEM) to estimate stopband characteristics, and a novel layer-based energy manipulation strategy to redirect energy, originating in excitation place, away from the output. The proposed approach is demonstrated to be effective for 3D RM design, through guiding the adjustment of geometrical parameters (GPs) of unit cells in each layer on 3D RMs. Moreover, the structure robustness is tested through experiments, facilitating the applications of 3D metamaterials.