Central Asia (CA) has attracted global attention because of either water scarcity or ecosystem degradation. The Amu Darya Delta (ADD), one of the most important oases in CA, is endowed with valuable wetlands and biological resources that provide good ecosystem services to inhabitants. However, the region has experienced climate warming and large-scale anthropogenic changes since the last century. To assess the influences of anthropogenic interventions on the soil environment in this area, surface soil samples collected from the ADD were analysed for aliphatic hydrocarbon fractions and five heavy metals (HMs; including Cd, Zn, Cu, Ni and V). The results indicated that the n-alkanes extracted from surface soils were composed of homologous series from C14 to C35. Relatively high abundances of short-chain n-alkanes (n-C33) occurred in most surface soils, which might be a sign of a hot and arid climatic environment. Notably, almost all samples presented a clear even carbon dominance of short-chain n-alkanes, especially for cluster 1, which possibly represented the influence of hydrocarbon contamination and highly saline carbonate environments in addition to bacterial degradation. The biomarker indices and HM enrichment index indicated greater effects of crude oil pollution on cluster 1 (specifically samples 2, 4, 5, 6, 13, 16 and 34) and anthropogenic activities such as traffic emissions and agricultural drainage on cluster 3 samples. The results of this study provide evidence that the n-alkane composition and abundance in surface soils respond sensitively to anthropogenic interventions, arid climate and petroleum hydrocarbon pollution.