Fritillaria unibracteata, a perennial herb, is a valuable and traditional Chinese medicinal plant. It is mainly distributed in alpine areas with an elevation above 3000 m. The bulb of this plant grows underground and is the part that is used medicinally. Unsustainable harvesting of this species has made it more valuable, which has greatly inflated the market price. This research study was carried out to help protect this rare and endangered plant, and to increase production in order to meet market demand. Two high mountains in the eastern Qinghai-Tibetan Plateau-Mounts Kaka and Niuniu were selected as our study sites. They are located in Songpan County, Sichuan Province, and are nearly 70 km away from the Jiuzhaigou Scenic Area. Eight 15 m×70 m plots were established on the slopes of the four cardinal directions (east-, south-, west-, and north-facing) of the two mountains. All plots were at 3800 m elevation. In each plot, 30 two-year-old F. unibracteata plants were randomly chosen for study. Then, data related to several ecological factors, including snow melting time, air temperature, soil water content, and soil pH, were measured on each slope of the two mountains. In addition, characteristics related to growth and reproduction of F. unibracteata were observed in detail and compared among the plants growing in the plots. The results showed that (1) snow melting time, air temperature, and soil water content significantly differed between south- and north-facing slopes, while soil pH did not differ significantly between the slopes of each mountain. (2) Three phenological phases (plant emergence, first flowering, and peak flowering) always began earlier in the year on south-facing slopes and later on north-facing slopes. However, the consenescence phase did not follow the same pattern as the three other phases mentioned above, because it began at nearly the same time on all slopes. (3) F. unibracteata plants growing on north-facing slopes had the largest leaf area and specific leaf area, and had the tallest stems, when compared with those on east-, south-, and west-facing slopes. Conversely, those growing on south-facing slopes had the smallest leaf area and specific leaf area, and the shortest stems. (4) For both mountains, the biomasses of the bulbs from the south-facing slopes were the largest, those from the north-facing slopes were the lowest, and bulbs from the east- and west-facing slopes were intermediate in size. (5) The mean biomass of fruit did not differ significantly among the four slopes, The ratio of fruit to aboveground biomass was largest on the south-facing slopes and smallest on the north-facing slope. (6) The number of seeds per fruit in plants from the north-facing slopes was the highest, whereas fruits from plants growing on the south-facing slopes had the smallest number of seeds per fruit. However, 1000-seed-weights were opposite to the number of seeds per fruit; that is, 1000-seed-weights in plants from the south-facing slopes were the heaviest and those from the north-facing slope were the lightest. In summary, these results support our conclusion that different slope aspects exerted an actual and strong influence on the growth and reproduction of this alpine species. In particular, most plant characteristics differed significantly in plants from the south- and north-facing slopes; and this should be considered when cultivating this species, so that the output of this herb can be increased and meet the needs of medicinal plant producers.