The apple trees, compared with farmland, has been applied larger amount of fertilizer, but they can extend roots deeper than 10 m below the ground. As such, the apple trees, as deep-rooted plants, have complicated effects on the nutrients in deep soils, but have not been fully evaluated. This study analyzed soil organic carbon (SOC), total nitrogen (TN) and total phosphorus (TP) variability and their controlling factors within 13-m profiles under farmland and apple orchards of different ages by field sampling in a typical loess-covered region of China. The results indicated that land use type and soil depth have combined effects on the variability of soil stoichiometry. Specifically, the mean contents of SOC and TN increased with the years for conversion of farmland to apple orchards, but those of TP had little change. Vertically, SOC and TN contents, ratios of C:P and N:P, declined in the 0-2 m range and then stabilized below 2 m, soil C:N ratio showed drastic change, but TP contents had minor variation with soil depths. The soil stoichiometries in shallow layers (0-2 m) showed insignificant correlation with soil properties, but those in the deep soil were significantly correlated with soil properties (p <=\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\le$$\end{document} 0.05). Overall, the soil nutrient content increased significantly after conversion of farmland to orchards, with the highest value under old orchards, but there were still problems of N and P limitation. This study is useful for soil nutrient management and environmental protection in arid regions.