AI agents have seen widespread adoption in information retrieval for scientific research, giving rise to tools such as Deep Research. However, existing retrieval agents mainly rely on keyword- or embedding-based methods. While effective at capturing content-level similarities, they struggle to understand complex relational networks among scientific papers, such as identifying corroborating or conflicting studies and tracing technological lineages. This fundamental limitation often results in fragmented knowledge structures, misinterpreted research sentiment, and ineffective modeling of collective scientific progress. To address this limitation, we introduce SciNet, the first Scientific Network relation-aware dataset for information retrieval agents. Built on a meta-database of 269 million papers across 7 disciplines and containing 8,940 carefully designed tasks, SciNet systematically captures three levels of relational understanding: ego-centric retrieval of papers with novel knowledge structures, pairwise identification of scholarly relationships, and path-wise reconstruction of scientific evolution. Extensive evaluation of three categories of retrieval agents shows that their accuracy on relation-aware tasks often falls below 20%, highlighting a fundamental shortcoming of current retrieval paradigms. Importantly, in a downstream literature review application, agents empowered with SciNet achieve a 25.3% improvement in review quality, highlighting the critical value of relation-aware retrieval for deepening scientific insights. We publicly release SciNet at https://github.com/tsinghua-fib-lab/SciNet to support future research.