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Soil ecological stoichiometry is essential for understanding nutrient cycling and ecosystem functioning in agricultural systems. However, how planting duration and crop type affect soil stoichiometric characteristics in protected cultivation systems across different agroecological zones remains unclear. Therefore, we selected 189 protected cultivation systems (PCS) and 130 adjacent open-field systems (OFS) in southern Shaanxi (SS), central Shaanxi (CS), and northern Shaanxi (NS) of Northwest China. The topsoil (0–20 cm) samples were collected in common cultivation durations (short-term cultivation, ST; medium-term cultivation, MT; long-term cultivation, LT) and crop types (leafy vegetables, LV; solanaceous vegetables, SV; fresh fruits, FF) plots to measure soil organic carbon (SOC), total nitrogen (TN), total phosphorus (TP), total potassium (TK), and other soil properties. The average ratios of C: N, C: P, and N: P for OFS were 14.37, 11.86, and 0.93, which were significantly different from 7.71 (C: N), 33.35 (C: P), and 4.38 (N: P) for PCS (P < 0.01). The key soil stoichiometric ratios (C: P, N: P, C: K, N: K) in both PCS and OFS were strongly modulated by agroecological zone, following a gradient of SS > CS > NS, while the soil C: N ratio in PCS ranged from 2.69 to 16.17. Cultivation duration significantly affected soil stoichiometric ratios of PCS, and its effects varied among agroecological zones. In NS, the C: K, N: P, N: K and P: K ratios of PCS under LT were 1.80, 1.56, 1.98 and 2.02 times those under ST, respectively. Crop type alone had limited effects except for N: K, but its interactions with agroecological zone and cultivation duration significantly affected C: N, C: K, N: K, and P: K. Partial least square structural equation modeling (PLS-SEM) indicated that soil stoichiometric ratios were influenced by agroecological zone, cultivation duration, and crop type through both direct pathways and indirect pathways mediated by soil properties. Furthermore, soil properties exerted stronger effects on soil stoichiometric ratios than agroecological zone or management factors. Therefore, this context dependence complicates attempts to generalize stoichiometric relationships but also highlights potential management strategies (e.g., K fertilization) for regulating soil nutrient balances across agroecosystems.