Secondary ion mass spectrometry (SIMS) is a promising tool to measure isotope ratios of individual uranium particles in environmental samples for nuclear safeguards. However, the analysis requires prior identification of a small number of uranium particles that coexist with a large number of other particles without uranium. In the present study, this identification was performed by scanning electron microscopy - energy dispersive X-ray analysis with automated particle search mode. The analytical results for an environmental sample taken at a nuclear facility indicated that the observation of backscattered electron images with × 1000 magnification was appropriate to efficiently identify uranium particles. Lower magnification (less than × 500) made it difficult to detect smaller particles of approximately 1 μm diameter. After identification, each particle was manipulated and transferred for subsequent isotope ratio analysis by SIMS. Consequently, the isotope ratios of individual uranium particles were successfully determined without any molecular ion interference. It was demonstrated that the proposed technique provides a powerful tool to measure individual particles not only for nuclear safeguards but also for environmental sciences.