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We examined the fruit morphology, oil content, and fatty acids (FAs) of 11 populations of <i>Swida wilsoniana</i> in four provinces in southern China. The fruit oil was extracted by the Soxhlet method, and the FA composition was determined by gas chromatography (GC). The variation in oil content ranged from 16.10 ± 4.94% to 33.08 ± 5.52%, and the major FAs were linoleic acid (44.85 ± 6.70%), oleic acid (29.45 ± 7.63%), palmitic acid (19.59 ± 3.98%), stearic acid (1.95 ± 0.39%), and linolenic acid (0.21 ± 0.07%). The unsaturated FAs accounted for 78.38 ± 3.74%. There was high genetic variation in the oil content and FA composition among the populations. We assessed the relationships between the ecological factors and the FA composition among the populations. The oil content was positively correlated with temperature (<i>r</i> = 0.645, <i>p</i> < 0.05) and negatively correlated with latitude (<i>r</i> = −0.653, <i>p</i> < 0.05). Interestingly, both latitude and temperature were strongly correlated with the unsaturated FAs of the fruits. Principal component analysis (PCA) showed that the populations in different areas could be separated based on oil quality and plant growth. In conclusion, the oil content and FA composition were influenced by geographical area. The findings could help to improve fruit oil quality in future <i>S. wilsoniana</i> breeding programs.