Resource limitation for soil microorganisms is the crucial factor in nutrient cycling and vegetation development, which are especially important in arid climate. Given that rock fragments strongly impact hydrologic and geochemical processes in arid areas, we hypothesized that microbial resource (C and N) limitation will increase along the rock fragment content (RFC) gradient. We conducted a field experiment in Minjiang river arid valleys with four RFC content (0 %, 25 %, 50 %, and 75 %, V V−1) and four vegetation types (Artemisia vestita, Bauhinia brachycarpa, Sophora davidii, and the soil without plants). Activities of C (β-1,4-glucosidase, BG), N (β-1,4-N-acetyl-glucosaminidase, NAG; L-leucine aminopeptidase, LAP), and P (acid phosphatase, ACP) acquiring enzymes were investigated to assess the limitations by C, N or P. In unplanted soil, the C acquiring enzyme activity decreased by 43 %, but N acquiring enzyme activity increased by 72 % in 75 % RFC than those in rock-free soils (0 % RFC). Increasing RFC reduced C:N and C:P enzymatic ratios, as well as vector length and vector angle (< 45°). Plants increased the activities of C and N acquiring enzymes in soils, as well as C:P and N:P enzyme activities, as well as vector length (by 5.6 %–25 %), but decreased vector angle (by 13 %–21 %). Enzyme stoichiometry was dependent on biotic and abiotic factors, such as soil water content, soil C:N, and total content of phospholipid fatty acids, reflecting microbial biomass content. Increased RFC shifted enzymatic stoichiometry toward lower C but stronger N limitation for microorganisms. Vegetation increased microbial C and N limitation, and impacted the enzymatic activities and stoichiometry depending on shrub functional groups. Consequently, the direct effects of vegetation, nutrient availability and microbial biomass content, as well as indirect effects of soil properties collectively increased microbial resource limitations along the RFC gradient.