Recently, Lycium ruthenicum attracted substantial attention due to the high value of its fruits to human health. As a result, the wild resources are at high risk of loss and detailed studies on the sexual reproductive ecology of this important medicinal plant should be conducted for better conservation. We investigated factors affecting reproductive output of the plant using six wild populations from Xinjiang. We compared differences in pollination frequency, pollinator composition, stigmatic pollen load, and ovule production among the populations, as well as correlations with reproductive output namely, fruit set, seed set and fruit production per plant. Results indicated that pollination frequency was significantly correlated with fruit set and seed set, and populations with high diversity in pollinator types had higher reproductive output. These results suggest that pollinator resource was one of the limiting factors affecting reproductive output. We also found that two populations, from Huaqiao farm, Hejing county (HJ3), and Huolashan valley, Yanqi County (YQ2), had unexpectedly low reproductive output. Detailed analyses indicated that flowers destroyed by sand-laden wind and artificial harvesting may also heavily reduce reproductive output. Our results provide valuable information for the conservation of this endangered plant and also on manipulation of artificial cultivation at a large scale.