Science is considered essential to innovation and economic prosperity. Understanding how nations build scientific capacity is therefore crucial to promote economic growth and national development. Although studies have shown that national scientific development is affected by geographic, historic, and economic factors, it remains unclear whether there are universal structures and trajectories behind national scientific development that can inform forecasting and policy making. By examining countries’ scientific exportation-the publications that are internationally indexed-we reveal a three-cluster structure in the relatedness network of disciplines that underpin national scientific development and the organization of global science. Tracing the evolution of national research portfolios reveals that while nations are proceeding to more diverse research profiles individually, scientific production is increasingly specialized in global science over the past decades. We further demonstrate that the revealed disciplinary clusters inform economic development, where the number of publications in applied research centered cluster significantly predicts economic growth. By uncovering the underlying structure of scientific development and connecting it with economic development, our results may offer a new perspective to study national scientific development and its relationships with economic development.