This experiment used greenhouse cucumber and tomato as experimental material to research the effect of the application of biogas residue，chicken manure and chemical fertilizer on soil microorganism quantity and enzyme activity and crop quality.The results showed that the biogas residue treatment reduced the number of fungi in the cucumber and tomato plant soils by 38.08% and 13.36%，increased the number of actinomyces by 17.91% and 66.67%，and increased the number of bacteria by 77.03% and 35.95%，respectively，compared to treatment with chemical fertilizer.Compared to treatment with chicken manure，the number of soil fungi was reduced by 16.58% and 5.05%，the number of actinomyces was increased by 7.14% and 60.49%，and the number of bacteria was increased by 26.28% and 21.40%，respectively.Thus，continuous application of the biogas residue treatment may transform the soils microecological structure from fungi to bacterial type，which may reduce the incidence of fungal diseases.At the same time，when compared with chemical fertilizer，biogas residue could effectively improve the cucumber，tomato continuous cropping soils invertase content，neutral phosphatase content and urease activity and subsequently improve the quality of cucumbers and tomatoes produced.Compared with chicken manure，biogas residue could effectively improve the soil invertase content and neutral phosphatase activity，though there was no significant influence on the quality of cucumbers and tomatoes produced.