To evaluate and predict the natural regeneration potential of shrub vegetation in dry valleys, we investigated the soil seed bank and its associated vegetation in the lower (Wenchuan valley), middle (Maoxian valley), and the upper reaches (Songpan valley) of the Minjiang River, using the “seed germination” method. Research sites covered by shrub vegetation are selected on south-facing slopes in the three valleys. Fifteen plots (2 m×2 m) at each site were established for soil seed bank investigation. Soil samples were taken according to soil surface, 0-5 cm and 5-10 cm soil depth. Vegetation investigation at each site was carried out in 15 plots with a size of 1 m×1m. A total of 4274 seeds belonging to 113 species were recorded in soil seed banks. The soil seed bank density was 102-103 ind./m2 and the number of species was 12-23 species/0.06m2. Both the mean seed density (ind./m2) and the mean number of species (species/0.06m2) were found to be lower in Maoxian, the middle reaches of the Minjiang River, than in the other two sites. Most of the species found in the soil seed banks and in aboveground vegetations at the three sites were perennial grasses. Most fruits found were achene, capsule and caryopsis with small seed size. The mean density and the mean number of species of soil seed banks were not correlated with the vegetation covered. The soil seed bank had low similarity (Sorensen′s index<30%) to its associated vegetation in species composition. The species richness in soil seed banks was higher than that in aboveground vegetations. Comprehensive analysis showed that the natural regeneration potential of the shrublands by germination of seed-banks in the dry valleys of the Minjiang River is low. Once the present vegetation is destroyed, the natural restoration of vegetations is hardly possible. Artificial restoration strategy in combination with natural regeneration should be employed, to accelerate recovery of vegetation. In addition, spatial heterogeneity of the existed vegetation and natural regeneration potential should also be considered. The present study provides foundational data for estimating the natural regeneration potential of vegetation and developing restoration and management strategy for vegetation in the dry valleys of the Minjiang River.