Seed mineral nutrition is essential for early seedling establishment, and varies under different environmental conditions. However, the intraspecific variation of multi-elements in seeds and the relative effects of climate and soil on seed elements remain unclear, even though understanding these factors is crucial for predicting plant reproductive responses to global changes. Here, we sampled seeds from Euptelea pleiospermum across 18 populations in China. We quantified the inter-population variation of 12 elements in the seeds and analysed their relationship with soil characteristics and climatic variables. We also explored the relationship of N and P concentrations between seeds and leaves. Results showed that seed elements were highly variable across different populations, with macroelements exhibiting lower variability than most of the microelements. Along the latitudinal gradient, the concentrations of K, Ca, Fe and Al in seeds increased, while the concentrations of C and Mn decreased. The stoichiometry of seed elements did not significantly correlate with latitude. Seed element concentrations were associated with both soil and climatic variables, and the influence of soil conditions on intraspecific variations is comparable to or even greater than climatic factors. However, seed stoichiometry was less related to environmental factors. Seeds had higher P but lower N than leaves, with no correlation between seed elements and leaf elements. Our findings suggest that mountain tree species respond to different local environments by adjusting seed element concentrations while maintaining relatively stable seed stoichiometry. We emphasize that, in addition to climate change, soil conditions should be considered when predicting the influence of environmental changes on the elemental composition of plant reproductive organs.