To investigate the mechanisms of associated cultivations on soil fertility and health, soil biological properties and microbial diversity in rhizospheres of tomatoes under associated systems were analyzed. The results showed that soil enzyme activities, such as Aminopeptidases and Phosphatase, and the soil microbial biomass carbon, nitrogen and phosphorus in rhizospheres of tomatoes were all significantly improved by associated cultivation with four associated crops except of flowering cabbages. In addition, although soil microbial diversities were not significantly improved by associated cultivations, but the proportions of microbial abundance at phylum or genus levels were altered. For example, the dominant bacteria at phylum level the abundances of Proteobacteria, Patescibacteria, and Firmicutes could be promoted by associated cultivations; Meanwhile, norank_f__Microscillaceae, norank_f__norank_o__ Vicinamibacterales, Bacillus, norank_f__Gemmatimonadaceae, and Altererythrobacter were the top ten dominant bacterial genera in rhizospheres of tomatoes under associated systems. Furthermore, compared with monoculture of tomato, soil fungal diversity and richness in rhizospheres of tomatoes under associated systems were also altered. Such as Phaeophyta, Streptomyces and Oleaginous at phylum level and unclassified_o__Sordariales, Olpidium,Conocybe, Phialemonium, unclassified_o__Pleosporales, unclassified_o__Boletales and Sodiomyces at genus levels not only enriched, but also the abundance of Chaetomium increases under associated systems. In conclusions, except of flowering cabbage, soil fertility and health in rhizospheres of tomatoes were all improved or maintained by associated cultivating with lettuce, amaranth, mint and green onion. In comparison to flowering cabbage, amaranth and green onion, lettuce and mint were the suitable associated crops for tomato.