Science is increasingly global, with international collaboration playing a crucial role in advancing scientific development and knowledge exchange across borders. However, the processes that regulate how scientific labor is distributed among countries remain underexplored, leading to challenges in ensuring both effective collaboration and equitable participation across diverse scientific communities. Here, we leverage three million internationally coauthored publications produced by countries worldwide to examine the division of scientific labor in international collaboration, identify the factors that shape this distribution, and assess its broader consequences. Our findings uncover a persistent hierarchical structure in international collaboration, with researchers from scientifically advanced countries tend to occupy leading roles, while those from less-developed countries are often relegated to supportive roles, even after controlling for various influential factors. This hierarchy is also reflected in the research content, as countries with lower scientific capacity tend to participate in international collaborations that deviate from their domestic science. By analyzing the labor division within international collaborations, we demonstrate that researchers from less-developed countries face systematic disadvantages, which not only limit their contributions to the global scientific community but also prevent them from fully benefiting from international collaborations.