Abstract: Physocarpus amurensis is an endangered shrub with an extremely narrow distribution in fragmented habitats. Its sexual reproductive capacity is low, and local population may be disappeared gradually. We studied the characteristics of pollination biology and breeding system of P. amurensis in the fragmented habitats through field observation and artificial pollination. Results showed that the life spans of single flowers and inflorescences were (5.1±0.23) d and (8.4±0.98) d, respectively. The flowering phase of a single flower can be divided into five periods in terms of flower morphology and dehiscence: “flower bud”, “pre-dehiscence”, “initial dehiscence”, “full dehiscence”, and “end-dehiscence”. Based on the results of pollen/ovule ratio, emasculation, bagging and artificial pollination studies, we found that the breeding system of P. amurensis is outcrossed and self-incompatible, and demands for pollinators. The fruit-setting ratio and seed-bearing ratio under natural conditions were low, (23.02±6.08)% and (9.86±2.86)%, respectively. The main reason might be that there are less species and quantities of pollinators and the pollination efficiency was lower in the fragmented habitats, suggesting that habitat fragmentation affects the early-stage reproduction success of P. amurensis. Artificial xenogamous pollination can significantly promote the fruit-setting and seed bearing ratios, reaching (60.17±4.67)% and (49.61±4.04)%, respectively.