Design of protected areas network (PAN) is one of the most effective way for biodiversity conservation. To realize long-term persistence of biodiversity, PANs should capture ecological and evolutionary processes that underpin the origin and maintenance of biodiversity. Under socio-economic limitations, spatial prioritization is a promising framework for developing effective PAN and could provide its feasible options. However, the existing prioritization method is mainly based on stacked range maps for individual species, but not explicitly accounts for macro-ecological processes of biodiversity patterns. Therefore, it is critical to assess process-based representativeness of PAN; how the existing prioritization methods capture the key biodiversity patterns that reflect species assembly processes (accumulation, turnover, and co-occurrence). In this view, we conducted spatial conservation prioritization analyses for eight taxonomic groups, including terrestrial and marine organisms, in the East Asian islands. Then, we compared various biodiversity metrics between the priority areas and the whole islands, and evaluated which biodiversity processes were (not) likely to be captured within the identified priority areas, in relation to the differences among the algorithms and/or taxonomic groups. Based on these results, we explored conservation plans for better emulating the mechanisms underpinning macro-scale biodiversity.