Abstract: Abstract: Continuous cropping difficulties have caused significant yield decrease in protected vegetable production system in China. It's been reported that the continuous cropping can result in the accumulation of autotoxin, the secondary salinization and acidification of soil in solar greenhouse. A variety of practices including grafting, crop rotation, and microbial agent application, have been used to improve the soil quality and enhance crop growth in protected vegetable production systems. The built-in straw biological reactor and microbial agents have been efficiently and widely used to alleviate the continuous cropping obstacles in China. The built-in straw biological reactor could increase crop production by enhancing the concentration of CO2 and soil temperature, while the microbial agents generally have positive effects on reducing the continuous cropping obstacles and decreasing soil-borne diseases. Tomato is one of the important vegetable crops in Chinese protected production systems. However, continuous cropping has caused obstacles of crop growth in protected tomato production systems. In this paper we studied the physicochemical properties and microbial diversities of tomato soils affected by four treatments. They are traditional management (CK), microbial agent (T1, 4 kg/667 m2), built-in straw biological reactor (T2, maize straw 4 t/667 m2 plus straw fermenting agent 8 kg/667 m2 plus composted pig manure 600 kg/667 m2), and the combination of microbial agent and the built-in straw biological reactor (T3, maize straw 4 t/667 m2 plus straw fermenting agent 8 kg/667 m2 plus microbial agent 4 kg/667 m2 plus composted pig manure 600 kg/667 m2). The study was conducted from 2009 to 2013. The over winter tomato was planted in a solar greenhouse in Fangshan, Beijing from October to next July each year. The soil samples of 0~30cm layers were collected at vegetative stage, early fruiting period, vigorous fruiting period and the last fruiting stage. Physicochemical properties including soil moisture content, pH and EC values, the mass fraction of organic matter, available P and K, and the microbial biomass C and N were determined. The functional diversity of microorganisms was analyzed using BIOLOG ECO Plates. The results showed that T2 and T3 treatments have higher soil moisture content and pH but lower EC values compared to control. T1 has low water content but has no effect on pH and EC. The straw biological reactor increased soil organic matter and microbial biomass, and decreased the contents of available P and K. However, a reverse trend was observed under the treatment T1. The treatment T1 improved the ability of utilizing polymers, carbohydrates and amino acids. The built-in straw biological reactor improved the ability of using amino acids, carboxylic acids, phenolic and amines. The combination of microbial agents and built-in straw biological reactor promoted the carbon catabolic ability of microorganism. All of three treatments improved tomato yield. These results indicate that the treatment T3 has the greater effect son soil improvement although has no apparent impacts on the yields. It is deserved to be promoted in greenhouse planting.