With the development of ecological agriculture and sustainable circular agriculture, greenhouse tomato plants develop rapidly in organic media culture. However, due to plant habitat requirements and reduction of production costs, the reuse of the cultivation medium has become common. As reuse increases, the influence that diseases and pests have increases, which decrease the yield and quality of fruits and impacts both the physical and chemical character, and so on. This becomes a major bottleneck that restricts the sustainable development of the greenhouse tomato in organic media culture. Self allelopathy is one of the most important obstacles to continuous cropping, commonly found in protected vegetable cultivation. Therefore, in protected tomato cultivation systems, the biological character and physicochemical character have an important theoretical and practical significance when exploring different enzyme activities in cropping rotation organic ecotype soilless culture media. This paper studied the effects of three cropping rotations (i.e. normal cropping, alternate cropping and continuous cropping) on the ellulase activity, polyphenol oxidase activity, invertase activity, dehydrogenase activity and pH, electrical conductivity and physical properties of the greenhouse tomato rhizosphere matrix in soilless culture. The results showed that substrate enzyme activities and pH, electrical conductivity and physical properties were strongly affected by the different cropping rotations. The absolute water content, invertase activity and dehydrogenase activity were the highest in normal cropping matrix and the polyphenol oxidase activity was the lowest. However, in the continuous cropping matrix, the substrate ellulase activity and polyphenol oxidase activity were the highest and substrate bulk density and pH were the largest. In soilless culture, the chemical properties in the substrate are closely related to the physical properties under normal cropping, alternate cropping and continuous cropping, leading to a change of micro-ecological environment, and finally resulting in continuous cropping obstacles. There was a poor correlation between dehydrogenase activity and the physical and chemical properties, but there were significant correlations of ellulase activity, polyphenol oxidase activity and invertase activity with the physical and chemical properties, which leads to a conclusion that the activities of sucrase, polyphenol oxidase and cellulase were the main factors influencing the pH, electrical conductivity and physical properties of the matrix. Under normal cropping, the plasticity index of the substrate, bulk specific gravity, total porosity and aeration porosity were statistically the greatest in all indexes, but the activities of dehydrogenase, polyphenol oxidase, fiber luciferase, absolute water content, total porosity, aeration porosity and void ratio plasticity indexes were the lowest when the tomato was continuously cropping. This leads to a conclusion that the normally cropped matrix has a very good and more extensive environmental adaptability than the succession cropping stubble. The plasticity index, void ratio, aeration porosity, dehydrogenase activity and absolute water content in all crops for rotation were greatest. Therefore, the void ratio, aeration porosity, dehydrogenase activity and absolute water content can be used to evaluate advantages of biological and physicochemical parameters in different rotation matrices. The observed results indicated that the different crops used for rotation have advantages as follows: normal cropping>alternate cropping>continuous cropping. Continuous cropping caused severe damage to the enzyme activity, biological and physicochemical characteristics of the matrix, while normal cropping has little effect on its biological and physicochemical parameters.