The article presents an innovative methodology for applying Semantic Web technologies to support fundamental geological research. The problem of semantic integration of heterogeneous geological data, characterized by different scales and interdisciplinarity, is considered. A five-stage methodology is developed, including domain analysis, ontological conceptual modeling, data transformation into a knowledge graph, deployment of a distributed data access infrastructure based on the conceptual model, and integration with processing and analysis procedures. Practical testing was conducted on three case studies: analysis of geochemical data for assessing territory pollution levels, creation of an information system about faults, and research on reservoir shoreline dynamics. The proposed ontological approach ensures compliance with FAIR principles and overcoming the "semantic barrier" in geological research. It is shown that Semantic Web technologies enable a transition from fragmented information arrays to a holistic semantic space of geological knowledge, opening new opportunities for generating comprehensive scientific hypotheses and cross-disciplinary research.