The tomato varieties of “shuiguowote” were used as experimental materials，and six different microbial agents were added into domestic and imported substrates respectively，the effects of different treatments on soil microorganism quantity，soil enzyme activity，tomato growth and fruit quality were observed after transplanting.The results show that:(1)In the domestic substrate mixed seedling，the number of bacteria and actinomycetes in rhizosphere soil was significantly increased，the number of fungi was decreased，and the total number of microorganisms was increased.However，the microbial diversity of tomato rhizosphere soil was not significantly affected by the inoculation with the imported substrate. (2)Although there was no significant effect on soil enzyme activities under two substrates，soil sucrase and alkaline phosphatase activities were the highest under the treatment of Caogen 8.(3)The plant height，stem diameter and chlorophyll content of tomato were the best when Caogen 8 was added.(4)Compared to CK，domestic substrate mixed with bacteria seedling treatment increased fruit weight，viamin C，lycopene，soluble sugar，and organic acid was significantly improved.However，there was no significant effect on fruit weight and fruit quality in the imported matrix mixed seedling. Principal component analysis showed that domestic matrix+Gaogen 8 treatment was the best treatment.In conclusion，the effect of domestic substrate on seedling breeding is better than that of the imported substrate.Domestic substrate+Caogen 8 treatment can achieve the purpose of increasing production and improving quality by changing the microbial community structure of tomato rhizosphere soil，increasing the number of soil bacteria and actinomycetes，reducing the number of fungi，optimizing the soil microbial community，enhancing the growth of tomato plants，and improving the green content of leaves.Therefore，domestic matrix+Caogen 8 is the best combination of matrix mixed bacteria for tomato seedlings.