<p><i>Malania oleifera</i> Chun &amp; S.K. Lee is an endangered tree species endemic to karst regions of southern China, valued for its seed oil with high nervonic acid content. To clarify soil nutrient levels and fertility conditions in wild <i>M. oleifer</i> habitats, this study applied principal component analysis (PCA) and the fuzzy membership function method to comprehensively assess soil fertility across different distribution areas. Results showed that soil pH had a low coefficient of variation, available phosphorus (AP) exhibited the highest coefficient of variation, and the remaining nine indicators showed moderate variation. The fuzzy membership function method identified available potassium (AK), available phosphorus (AP), available iron (AFe), and available copper (ACu) as the primary limiting factors for the soil fertility quality of <i>M. oleifera</i>. PCA and fuzzy membership function assessments yielded broadly consistent results: exchangeable calcium (ECa), available nitrogen (AN), exchangeable magnesium (EMg), organic matter (OM), and available zinc (AZn) were key indicators of soil comprehensive fertility. When the integrated soil fertility index (IFI) was classified into five grades via systematic cluster analysis, the fuzzy membership function method achieved better soil grade differentiation. In summary, soil of <i>M. oleifera</i> stands in Guangnan County is predominantly weakly acidic, and the species exhibits a calcicolous growth habit. Based on the identified limiting nutrients, it is suggested that appropriate applications of phosphorus, potassium, organic fertilizers, and calcium–magnesium amendments may help improve soil fertility in specific stands.</p>