Development from bare soil to biological soil crust (BSC) after the establishment of vegetation for sand fixation is an important desertification rehabilitation process in dryland ecosystems. While subsequent changes above-ground have been well documented, few studies focused on how BSC affects soil food webs after vegetation establishment. In this study, we investigated how soil food web channels respond to BSC, and in particular how flow of carbon from microbes to higher trophic levels is affected in Horqin Sandy Land, China. The BSC layer and 0-1 cm depth soil layer without BSC (as the control of BSC) were taken. After that, soil samples of 10 cm depth were collected and then dividing into two equal 5 cm parts for comparing soil microbe and nematode community composition in 2013 and 2014. The results showed that presence of BSC increased the phospholipid fatty acid and biomass carbon of microbes in the top layer of both years. Abundance, biomass carbon, and metabolic footprint of nematode trophic groups, induding fungivores and omnivores-predators in the top layer, had higher values under BSC. Positive relationships were found between total organic carbon of BSC and biomass carbon of fungi, and between biomass carbon of fungi and fungivores. BSC enhanced carbon flow from fungi to fungivores, with higher connectance values in the fungal channel than in soil without BSC. The strengthened relationships between total organic carbon of BSC and omnivore-predator, and high connectances of the fungal channel and of the omnivore-predator channel under BSC, suggest a more reticulated charmel in soil food web. It can be concluded that colonization of BSC enhances the connenctances in soil microbial food web channels, and could contribute to the resilience of dryland ecosystems.