To reframe the imperfect review processes of nation-scale actions on area-based conservation through protected area (PA) networks, we first created novel infrastructure to visualize nation-level biodiversity information in Japan. We then assessed the performance of the existing PA network relative to land exploitation pressure and evaluated conservation effectiveness of PA expansion for the post-2020 Global Biodiversity Framework. The Zonation algorithm was used to spatially prioritize conservation areas to minimize biodiversity loss and the extinction risk for 8,500 Japanese vascular plant and vertebrate species under constraints of the existing PA network and land use. The spatial pattern of the identified priority areas, which were considered candidate areas for expansion of the current PA network, was influenced by land-use types according to the mask layers of non-PAs, and low-, middle-, and high-ranked PAs. The current PA network reduced the aggregate extinction risk of multiple species by 36.6%. Indeed, the percentage of built-up areas in the existing PAs was in general smaller than that in the areas surrounding PAs. Notably, high-ranked PAs fully restrained built-up pressure (0.037% per 10 years), whereas low-ranked PAs in the national park and wild-life protection areas did not (1.845% per 10 years). Conservation effects were predicted to substantially improve by expansion of high-ranked (legally strict) PAs into remote non-PAs without population/socio-economic activities, or expansion of medium-ranked PAs into agriculture forestry satoyama and urban areas. A 30% land conservation target was predicted to decrease extinction risk by 74.1% when PA expansion was implemented across remote areas, satoyama, and urban areas; moreover, PA connectivity almost doubled compared with the existing PA network. In contrast, a conventional scenario showed that placing national parks in state-owned and non-populated areas would reduce extinction risk by only 4.0%. The conservation prioritization analyses demonstrated an effectiveness of using a comprehensive conservation approach that reconciles land-sparing protection and land-sharing conservation in other effective area-based conservation measures (OECM) in satoyama and urban green spaces. Our results revealed that complementary inclusion of various PAs interventions related to their governance and land-use planning plays a critical role in effectively preventing biodiversity loss and makes it more feasible to achieve ambitious conservation targets.