Crude oil contamination remains a major environmental challenge in oil-producing regions, causing profound alterations in soil quality and threatening the productivity of economically important crops such as Hevea brasiliensis. This study evaluated the effects of varying crude oil contamination levels (0, 1, 3, and 5% w/w) on soil physicochemical properties, elemental composition, hydrocarbon accumulation, and the biochemical characteristics of rubber saplings cultivated for 26 weeks. Soil physicochemical parameters, inductively coupled plasma–optical emission spectrometry (ICP–OES), Fourier transform infrared spectroscopy (FTIR), and scanning electron microscopy coupled with energy-dispersive X-ray spectroscopy (SEM–EDS) were employed to characterize contamination-induced changes. Increasing crude oil concentration significantly (p < 0.05) acidified the soil (pH 6.85–5.51), elevated total petroleum hydrocarbons (45.2–6,920 mg/kg) and electrical conductivity (182.4–402.8 µS/cm), while reducing nitrogen, available phosphorus, moisture content, cation exchange capacity, and essential exchangeable cations. ICP–OES revealed progressive accumulation of Fe, Zn, Cu, Pb, Cd, Cr, Ni, V, As, and Na in both soils and plant tissues, whereas Ca, Mg, K, and Mn declined significantly with increasing contamination. FTIR spectra demonstrated progressive enrichment of aliphatic hydrocarbon functional groups and shifts in hydroxyl- and carbohydrate-associated bands, indicating biochemical modification of plant tissues. SEM–EDS analysis further confirmed contamination-induced structural deterioration and alterations in elemental distribution within rubber saplings exposed to higher crude oil concentrations. Collectively, the findings demonstrate that crude oil contamination substantially degrades soil quality, promotes uptake of potentially toxic elements, and induces marked biochemical and structural changes in H. brasiliensis. These results provide important insights into the mechanisms of crude oil toxicity in rubber cultivation and offer a scientific basis for developing sustainable remediation strategies for contaminated plantation soils.