Xanthoceras sorbifolium with high oil content in seeds has been used for various purposes, including as edible oil and feedstock for biodiesel production; however, the large-scale commercial cultivation of this species is severely hindered by the poor seed yield. As a self-incompatible species, whether a suitable pollen source can effectively improve yield and fruit traits of super clones has not been confirmed in X. sorbifolium. In the present study, cross pollination, mixed pollination, and natural pollination were conducted in five super clones. For all clones, the highest pollen germination was observed one day before flowering 84.26–90.25% (**p < 0.01). The final fruit set ratio (FFSR) was significantly influenced by the pollen source (*p < 0.05). Hand pollination had a positive effect on FFSR and seed yield (*p < 0.05). Fruit width and 1000-seed weight were significantly influenced by pollen source (*p < 0.05). Fruit weight, length, seed number per fruit, seed-producing ratio, seed yield, seed size, kernel ratio, and chemical components were significantly affected by the recipient × pollen source (**p < 0.01). In all combinations, the maximum seed yield occurred in the combination No. 2 × No. 3. The xenia effect occurred in the 1000-seed weight and kernel starch concentration. Based on these traits, the most suitable pollen source for each super clone was identified. This study suggests the significance of a suitable pollen source and collocation of pollinizer trees, especially in X. sorbifolium plantations, which can be applied in its cultivation and yield improvement.