Elaeagnus angustifolia L. is a highly adaptable urban ornamental plant, playing a key role in dry land and saline-alkali protective forests. The diverse geographical and climatic conditions in Gansu Province have resulted in variations in its distribution and growth. This study assesses the phenotypic diversity of fruits and seeds, and the seed germination characteristics of 82 E. angustifolia plants from nine populations in Gansu Province, exploring their relationship with geographical and climatic factors. We measured 12 phenotypic traits and five germination indices. This study included germination tests under standard conditions, statistical analysis of phenotypic differences, and Pearson and Spearman correlation analyses to examine relationships between traits and geo-climatic factors. Principal component and cluster analyses were also performed to identify key traits and classify populations. The findings were as follows: (1) Significant differences were observed in phenotypic traits and germination characteristics among populations. Single fruit weight showed the highest variation (27.56%), while seed transverse diameter had the lowest (8.76%). The Lanzhou population exhibited the greatest variability (14.27%), while Linze had the lowest (6.29%). (2) A gradient change pattern in traits was observed, primarily influenced by longitude and a combination of geographical and climatic factors. Seed germination was positively correlated with altitude, annual precipitation, and relative humidity, but negatively affected by latitude and traits such as fruit weight. (3) Principal component analysis identified germination rate, germination index, seed shape index, and fruit shape index as primary factors, contributing 27.4%, 20.6%, and 19.9% to the variation, respectively. Cluster analysis grouped the 82 plants into four clusters, not strictly based on geographical distance, suggesting influence from factors such as genotype or environmental conditions. In conclusion, this study lays a foundation for understanding the genetic mechanisms behind the phenotypic diversity and germination characteristics of E. angustifolia. It offers insights into how geo-climatic factors influence these traits, providing valuable information for the species’ conservation, cultivation, and management.