Biocrusts may affect seedling emergence and growth through direct or indirect pathways. However, most of the relevant studies have been conducted in extremely arid deserts using flower pots. To clarify whether biocrusts promote or inhibit early vegetation establishment in a relatively natural environment and to identify the pathways, we established field plots on cyanobacteria- and moss-dominated crusts, treated the biocrust cover as high, middle and low (80%, 50% and 30%) and sowed the seeds of Caragana korshinskii, Artemisia ordosica and Bidens pilosa on the surface of plots. Seedling emergence percentage, survival percentage and growth rate were then calculated. The results showed that the high-cover biocrusts were more favourable for seedling emergence. In comparison to bare soil, the seedling emergence percentage of Caragana korshinskii and Artemisia ordosica increased by 1.5 and 17.5 times on high-cover moss crusts, respectively, and by 1.3 and 14.0 times on high-cover cyanobacteria crusts. The seedling emergence percentage of Bidens pilosa increased by 0.7 times on high-cover cyanobacteria crusts. However, the survival percentage of Artemisia ordosica seedlings on biocrusts was extremely low. This means that the biocrusts are beneficial for seedling emergence of small seeds, but detrimental for their survival. Overall, moss crusts increased the growth rate of seedling height and ground diameter, with the greatest enhancement on high-cover moss crusts. While cyanobacteria crusts showed promotion at high cover and inhibition at middle and low cover. Structural equation model analysis showed that the biocrusts affected seedling emergence and growth mainly through indirect effects, and the total effects were positive. The penetration resistance was the main factor promoting seedling survival, and the soil chemical property was the main factor promoting seedling growth. In summary, the effects of biocrusts on seedling emergence and growth differ between plant species, and the effects are related to biocrust cover. But in general, the effects are favourable, making biocrusts are beneficial for vegetation restoration and regeneration on the Loess Plateau.