Although many studies have been conducted on the ecological functions and ecophysiological characteristics of lichen soil crusts (LSCs), no explanation of these results has been provided based on crust structures. Using algae soil crusts (ASCs) as comparison, this work studied the small-scale vertical distribution of algal biomass and stratification in two types of LSCs, by combining the binocular stereomicroscope observations, microscope observations, plate cultures, chlorophyll analysis, and polysaccharides analysis. The results showed an obvious difference in the proportion but not the composition of the algae species between the ASCs and the two LSCs. Approximately 60% and 80% of the total algal biomass were concentrated in the top 1 mm of the soil profile and thalli in the ASCs and LSCs, respectively. This implies that symbiotic algae are the dominant species and primary organic carbon producers in LSCs, and the algal biomass decreased with the depth in both the ASCs and LSCs. The small-scale vertical distributions of the crustal algal biomass and polysaccharides were characterized by obvious successional stage, whereas these were unrelated to the crust type within the successional stage. Additionally, a large amount of fungi, which were always piercing the entire crusts, were observed in the LSCs, but only occasionally in the ASCs. These special structures are purported to cause the LSCs to achieve specific ecological functions, such as higher carbon fixation and greater compressive strength. High biomass, large living space, and advantageous resource utilization privilege suggest that the lichen association is mutualistic and the direction from ASCs to LSCs is developmental.