Organelle genomes serve as crucial datasets for investigating the genetics and evolution of plants and animals, genome diversity, and species identification. To enhance the collection, analysis, and visualization of such data, we have developed a novel open-source software tool named Organelle Genome Utilities (OGU). The software encompasses three modules designed to streamline the handling of organelle genome data. The data collection module is dedicated to retrieving, validating, and organizing sequence information. The evaluation module assesses sequence variance using a range of methods, including novel metrics termed stem and terminal phylogenetic diversity, as well as observed resolution. The primer module could design universal primers for downstream applications. Finally, a visualization pipeline has been developed to present comprehensive insights into organelle genomes across different lineages rather than focusing solely on individual species. The performance, compatibility, and stability of OGU have been rigorously evaluated through benchmarking with four datasets, including one million mixed GenBank records, plastid genomic data from the Lamiaceae family, mitochondrial data from rodents, and 308 plastid genomes sourced from various angiosperm families. Based on software capabilities, we have identified 30 plastid intergenic spacers that exhibit a moderate evolutionary rate and offer practical utility comparable to coding regions, which highlights the potential applications of intergenic spacers in organelle genomes. We anticipate that OGU will substantially enhance the efficient utilization of organelle genomic data and broaden the prospects for related research endeavors.