Germanium has application prospects in both industrial and medical fields, organogermanium compounds exhibit low toxicity and antitumor activity. It is valuable to develop Ge-rich soil, whereas the research on soil Ge is still insufficient in China. Based on multi-purpose regional geochemical survey in Guangxi, the authors studied the spatial distribution of Ge in top soil and deep soil in Beibu Gulf in this paper. The Ge values of top soil as well as deep soil derived from various parent materials were elucidated, and the factors that influence soil Ge content were summarized. The results show that the average values of Ge in top soil and deep soil are 1.43 mg/kg and 1.64 mg/kg, respectively. The Ge values are critically controlled by parent materials, and the soil derived from carbonates has the highest Ge content, followed by soil that has originated from granites, Quaternary sediments, sandstones and shales. The ratios of top soil Ge values and deep soil Ge values indicate that Ge values of top soil are effected little by anthropogenic activities. The influencing factors of Ge contents vary in soils derived from different parent materials. As for top soil and deep soil derived from granites, Ge values are primarily influenced by clay minerals, gibbsite and quartz in soil. In contrast, for soils derived from carbonates, Quaternary sediments, sandstones and shales, top soil Ge values are primarily influenced by clay minerals, gibbsite, secondary Fe-bearing minerals, amorphous Fe oxyhydroxides, quartz and organic matters in soil, and deep soil Ge values are primarily influenced by clay minerals, gibbsite, secondary Fe-bearing minerals, amorphous Fe oxyhydroxides and quartz in soil. 53.32% of top soil have a slightly-rich level of Ge values and 30.21% of top soil have a rich level of Ge values, which are beneficial for Ge-rich agricultural crops cultivation and worthwhile for further exploitation. The objects of this study are to provide basic information for Ge ecogeochemistry, support Ge-rich soil and agricultural products development.