<p>The advent of intestinal organoids has fundamentally transformed biomedical research by providing a physiological ex vivo model that recapitulates native tissue architecture. Despite an exponential surge in publications, a comprehensive mapping of the field’s evolutionary trajectory remains lacking. This study employs bibliometric analysis to dissect the global landscape of intestinal organoid research from 1986 to 2025, utilizing data from the Web of Science Core Collection. By leveraging VOSviewer and bibliometrix tools, we demonstrate that while the USA dominates in publication quantity, the Netherlands commands the highest citation influence, reflecting the enduring legacy of foundational works by Sato and Clevers. Co-citation and keyword trend analyses demonstrate evolving research priorities. The field initially focused on stem cell differentiation and culture optimization, then expanded into disease modeling of colorectal cancer and inflammatory bowel disease. Notably, recent burst detection identifies a clear pivot towards “organ-on-a-chip” technology, “mechanobiology,” and “single-cell sequencing”. These hotspots signal the advent of precision engineering. Bioengineering and high-throughput omics together drive the development of next-generation physiologically relevant intestinal models. Ideally, this bibliometric blueprint serves as a navigational guide for researchers, highlighting the paradigm shift towards complex, engineered micro-physiological systems (MPS) as the future of intestinal research.</p>