<p>The application of ecosystem services (ES) theories in land consolidation is a confusing issue that has long plagued scholars and government officials. As the upgraded version of traditional land consolidation, comprehensive land consolidation (CLC) emphasizes ecological benefits, but it does not achieve the expected effect during the pilot phase. This study first proposed a theoretical analysis framework based on ES knowledge to answer the three key questions of why, where, and how to implement CLC better. Taking mountainous counties as the study area, we found that ES trade-offs/synergies, bundles, and drivers were significantly affected by scale effects. ES knowledge can play a crucial role in designing multi-scale CLC strategies regarding the objective, zoning, intensity, and mode. Specifically, mitigating the significant trade-offs between recreational opportunities, food production, and other ES is the top priority of CLC. Land consolidation zoning based on the ES bundles analysis is more rational and can provide the scientific premise for designing locally adapted CLC measures. Land consolidation can be classified into high-intensity direct intervention and low-intensity indirect intervention modes, based on the major drivers of ES. These findings help narrow the gap between ES and CLC practices.</p>