Abstract: To slow down the secondary salinization of protected cultivation soil and improve the soil quality, we carried out long- term irrigation of magnetized water in protected cultivation soil, set up 2 treatments (magnetized and non-magnetized water irrigation) by field tests, and determined the physiochemical property of 0-15 cm layer and the quality of Capsicum frutescens. The results showed that: (1) the contents of vitamin C, anthocyanin, reducing sugar and soluble sugar increased by 1.76% to 46.85%, whereas the content of organic acid decreased under the magnetization treatment (MT) compared with that under the non- magnetization treatment (NMT); (2) the magnetization treatment increased the content of Fe, Cu, N and P in the leaves, which was higher than that of the fruits, while the content of Mn and Zn was lower in leaves than that in fruits; (3) the MT reduced the total content of N, P, Mn and Zn by 2.04%-20.61%, increased the total content of Fe and Cu by 4.64%-6.48%; decreased the ion exchange amount of K, Na and Ca by 2.15%-4.95%, whereas increased the ion exchange amounts of Mg; compared with those of NMT, the available content of nitrat, ammonium nitrogen, available phosphorus and organic matter were improved by 17.64- 113.39% under MT; (4) MT increased the activities of urease, sucrose enzyme, phosphatase and catalase by 0.27%-24.75%; (5) the soil bulk weight decreased and the porosity increased under MT, the content of clay and powder increased, but the content of sand decreased. In conclusion, the irrigation with magnetized water is benefit for improving the soil physiochemical properties and promoting the quality of fresh pepper fruits.