For straw incorporation, three crucial factors affect the soil microbial community and various enzyme activities: straw length, amount and burial depth. To analyse the individual and interactive effects of these three factors on the soil microbial community and various enzyme activities, 23 treatments with five levels of the three variables (straw length, amount and burial depth) were applied in a quadratic orthogonal rotation combination design. A comprehensive indicator was constructed that could represent soil microbial functional diversity and enzyme activity by determining the weights of measured indicators and using Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS). The results indicated that the soil microbiological indicators have a higher criteria weight than soil enzyme activity indicators. The final weight orders of indicators were as follows: Shannon–Weaver > invertase > Shannon evenness > urease > catalase > McIntosh index > Simpson diversity > phosphatase. The soil comprehensive values constructed by the TOPSIS method are reliable. The optimal combination for the improvement of soil microbial functional diversity and enzyme activity was a straw length of 13–24 cm, burial depth of 10–17 cm and straw amount of 370–650 g/m2.