Whether genotypic diversity within a dominant species plays a pronounced role in community and ecosystem processes similar to species diversity is a hot research topic in population ecology. Such studies will benefit the conservation and restoration of population or community. We collected soils from the previously established Leymus chinensis populations of different genotype combinations (1-, 3-, 6-genotype) under different interference intensities (no mowing, 10 cm stubble and 5cm stubble), to study the effects of genotypic diversity of L. chinensis population and the interferences on community composition and structure of soil macrofauna and phospholipid fatty acid (PLFA) biomarkers of soil microorganisms. The results showed that the interaction of genotypic diversity and disturbance intensity significantly impacted the amounts of groups and individuals of soil animals (P<0.05). Under 10cm stubble condition, there was a significant positive correlation between the amounts of soil animal individuals and the number of L. chinensis genotype (P<0.05), which supported partly the “resource specialization hypothesis”. The effects of genotypic diversity on soil microbial community composition and structure were significant under no mowing condition (P<0.05).