Planting alfalfa is one of the biological measures to manage the Pisha stone area in the Yellow River Basin, where soil erosion is serious, and the ecosystem is extremely fragile. The characteristics and driving factors of plant-soil ecological stoichiometry during the planting process of the loess layer (LL) (0-90 cm) and Pisha stone layer (PSL) (90-180 cm) were studied to reveal the limiting factors of plant-soil nutrients and the driving mechanism of ecosystem evolution in this area. In this study, the correlation between the contents of carbon (C), nitrogen (N), phosphorus (P), and their ratios in alfalfa and soil with different planting years (2, 5, 8, and 10 yr) was measured. Plant-soil C, N, and P stoichiometry characteristics were explored to analyze the influence mechanisms of fallow years and soil layers. The results showed that the changes of C, N, and P in alfalfa were similar to those of soil organic carbon (SOC), total nitrogen (TN), and total phosphorus (TP) in LL. Alfalfa C/N was significantly positively correlated with soil C/P and N/P. Alfalfa growth is limited by N in the early stages and P in the middle and late stages, which can provide a theoretical basis for vegetation restoration and soil erosion management in the Pisha stone region. This study investigated the stochastic properties of the alfalfa-soil continuum and its fluctuations with the planting year.